does my affiliation affect the decision of accepting my paper in a journal Many times, you receive comments such as:I am unable to accept your manuscript for publication in "Journal name" The reason for this decision is that in its current state, the level of English throughout your manuscript does not meet the journal's required standard.
The work was revised thoughtfully and reach reviewing stage in higher impact journal but was not accepted because of scientific disagreement.
You seem to be asking if it is possible that due to your affiliation, your paper is rejected for bogus reasons.

While this cannot be ruled out with certainty, such cases should be very rare in reputable journals. Reviewers are advised to only take the scientific content and the clarity of the presentation into account.

It is quite common that a presentation that is quite hard to follow makes the reviewer unable to assess the scientific contribution. This is because the reviewer shouldn't guess what is meant to make her/his judgment. If a central part is unclear, then this precludes the reviewer from supporting acceptance. If a follow-up submission is made with an improved presentation,  only then, the reviewers can check the scientific content properly and recommend to accept or reject the paper. Getting the improved version rejected (again) is not a sign of discrimination, but rather one should see the first try as a paper draft that has not actually been reviewed due to lack of clarity.

Note that many scientific communities are close-knit, so if an author needlessly does not adhere to the standards of the community in terms of the type of experimental evaluation, the arguments used, or the questions being answered, then this can also lead to little interest by the journal to accept a paper.