Well, it might.
They look at all evidence of a shared marital life, and joint tax returns are considered very strong evidence. The question is, how strong is your other evidence? With lots of other shared financial and other documentation - joint accounts, utilities, lease, insurance, estate planning, etc. - you may be approved even if you filed taxes separately.
But, you need to have an attorney evaluate your case.
I always advise my clients to file income taxes in whatever way you can legally get the largest amount back. Do not let an accountant simply tell you that you will get more back if you check a certain box on the return. Make sure that what the accountant is doing is proper for a married couple. You should definitely speak with an immigration attorney to make sure that you are not hurting your case - it will depend on what other evidence you have.
The above is not intended as legal advice.