These mistakes are very commonly made when authors write their scientific paper. They increase the risk of rejection, especially when many of these errors are present. The following table will list these mistakes, explain why they are problematic, and how they can be avoided. 

In addition to the hints given here, I should point out that many of these mistakes can be avoided by checking the relevant study reporting guideline for the reporting structure and elements that your paper will need. I have also created a simplified guideline for reporting human observational studies that includes relevant STROBE and CONSORT guidelines.

Part of paper
The mistake
Comment
How to avoid this mistake
ABSTRACT1. Abstract lacks one or more key elements
  • Background
  • Purpose of the study/paper
  • Type of study (animal, lab, RCT, cross-sectional, case series etc)
  • ALL key methods
  • ALL key findings (NEVER mention data in the Abstract that are not described in the Results)
  • A brief conclusion

The Abstract is the most read part of your paper. It is essential that it contains ALL of the key elements and messages of your paper. Check that ALL elements required are included. CONSORT for Abstracts gives good guidelines for not just randomized controlled trials but also observational human studies in general
INTRODUCTION, DISCUSSION, REVIEWS 2. Studies cited in these literature-based papers/paper parts are not fully described
(a) Type of study is unclear (e.g. RCT, cross-sectional, case report, in vitro, animal study, in silico study)
This makes it difficult for the reader to determine the quality of the evidence for the claim being made. Is it reliable (RCT, large prospective cohort study) or weak (case report, in vitro study?)Check that the study type and its important elements are fully described

(b) Type of subject unclear:
  • type of animal in animal study
  • type of cell in in vitro study
  • in human studies, type of patient (e.g. >75 yo community dwellers), cohort size, mono/multicentric study, prospective/retrospective study etc.
This makes it difficult to see how comparable similar studies areCheck that the study type and its important elements are fully described

3. References are incorrectThis mistake is unnecessary and it gives the impression of sloppiness. That could make the reviewer distrust everything about the paper.Check that all references are appropriate and correctly cited

4. References are not the ORIGINAL source of the data supporting the claim/statement in your paperThis can lead to unreflected dogmas in the  field that have not actually been tested experimentally. These unchallenged dogmas can be quite destructive to the progression of scienceTry as much as possible to make sure that the cited paper provides original data supporting the statement

5. Accidental plagiarismThis is because of copy and paste and then not reformulating. Copy-paste is a common technique for extracting information from the literature but if not rewritten, it is often clearly detectable to readers and may trigger journal plagiarism softwarePut the copied-pasted text in a color and then, when revising the text, make sure that only one in three/four words remains that color
METHODS6. No/poor ethics sectionHaving a well-written and detailed ethics section gives the reader confidence that you understand the importance of ethics in biomedical scienceAll studies: "This study was approved by [the appropriate] ethics committee/institutional review board"
Human studies: "This study adhered to the tenets of the Declaration of Helsinki and its revision"; "This study adhered to Good Clinical Practice guidelines"; "All patients provided written/oral informed consent to have their data included/ to participate in the study"
Animal studies: "This stu
dy was conducted according to international [e.g. Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC International)], national, and/or institutional guidelines for humane animal treatment and complies with [relevant] legislation"  

7. Human study design not stated or incorrect  (e.g. Cohort when it is cross-sectional)Disclosing the study type helps the reader to quickly estimate the likely quality of your study findings. Not adding this information or using the wrong label may make the reviewer think that your understanding of study design could be limitedIf unsure, consult the Equator Network to determine what type of study your study is

8. Not stated when the study in humans was conducted (e.g. January 2014-March 2015)Was the study performed last year or two decades ago? This is particularly important for clinical studies because clinical practice can change very markedly over timeMake sure that you indicate when the study was performed in the Abstract and Methods

9. Experimental timelines unclear e.g. when after the intervention did treatment start and when were samples taken? How long was follow-up? These experimental details should be described very clearly so that the reader knows how the experiment/study proceededClearly describe these experimental details in the Abstract and Methods. Consider using a schematic depiction of the experimental timeline if multiple intervention timepoints and/or sampling timepoints are used

10. Detailing patient numbers in the Methods section e.g. “1022 patients were enrolled and 19 were excluded”The Method section in human studies should only describe HOW the patients were selectedOnly describe patient numbers in the Results section. Animal/well/cell numbers can be indicated in the Methods if the same number are used for all experiments. If varying animal/well/cell numbers are used, indicate this in the figure legends

11. Primary and secondary outcomes are unclearThe primary outcome MUST be clearly indicated because the power calculation determining the optimal study sample size should be based on being able to detect a a significant different regarding the primary outcome. This is often a confusing area in the MethodsMake sure to clearly distinguish between primary and secondary outcome measures in the Abstract and Methods

12. No power calculationDoes the study have enough power to detect a difference in primary outcome? Otherwise, the study is essentially uselessConsult a statistician to determine the optimal sample size. If necessary, a post-hoc analysis can be performed (but a priori power size calculations are better)

13. Statistics section incomplete/unused stats methods mentionedThis makes the reviewer think you do not understand your statisticsMake sure the Statistics section clearly explains ALL statistics you used and which analyses were performed
METHODS & RESULTS14. Use of uninformative experimental group namese.g. Group 1, 2, and 3. The reader has to work hard to remember which is the control, which is intervention A, which is intervention B etc
Generally, group names are NOT needed. If absolutely necessary, use short, memorable, and completely distinguishable groups names

15. Use of complicated experimental group namese.g. a study in rats where the sciatic nerve is denervated surgically and then half of the rats start exercise training (ET) at 2 or 6 weeks. Groups are called Den2w, Den6w, Den2wET, Den6wET. It can be very confusing for the reader
Generally, group names are NOT needed. If absolutely necessary, use short, memorable, and completely distinguishable groups names
RESULTS16. Describing experiments that have not been mentioned in the Methods (or vice versa)Many readers will quickly skim through the Methods before moving onto the Results. If an experimental method is suddenly mentioned in the Results but the method was not detailed in the Methods, this can confuse the reader Make sure that all methods used to get the results are actually described in the Methods (and vice versa)

17. Describing data that do not relate directly to the study objective. Often people do this because these data are not sufficient to write a whole paper aboute.g. cohort study examining whether 800 patients with rheumatoid arthritis on MTX mount good antibody responses to flu vaccine A. A subgroup of 20 patients is examined for T-cell responses to flu vaccine B antigen. 
The subgroup analysis will distract the reader from your main findings, disrupt the smooth flow of concepts, and cause confusion
Make sure that ALL data relate directly to the study question

18. Unclear how many patients/animals/wells per experiment, and how many times the experiment was performedThis is Science101 basic information that should always be included because it shows how reliable the findings areAlways indicate how many patients/animals/cells/wells were used for each experiment in the Results (human studies) or figure legends (other studies)

19. Inconsistencies between the Results section (and/or Abstract) and the data shown in the tables and figures

e.g. Results: “Of the 93 patients who received the study drug, seven (7.5%) had developed new-onset hypertension at 3 years.”

Table 1:

This kind of mistake is sloppy and can cause the reader to distrust your paper, especially when the p value is close to not being significant. The reader may become suspicious that the data were massaged
Always check that all data cited in the Abstract and Results match completely with the data in the figures and tables
DISCUSSION20. No Study Limitations section

No study is perfect - all have flaws e.g.

  • What are the limitations of the study design? e.g. a cross-sectional study shows that people with high alcohol consumption are more likely to have cirrhosis  <-- Causality hypothesis must be tested by other study designs
  • Was the sample size large enough?
  • Did the patient eligibility criteria introduce selection bias?
  • How generalizable is your monocenter patient cohort to patients in other hospitals?
  • Was your mouse model a good model for the disease?

It is essential that you are completely open about the limitations of your study. It makes you look very trustworthy and shows that you are really interested in answering the scientific question