How does the fender fit without the gaskets? The gaskets are anti-squeak, so they need to be somewhat thick. How thick are they?
Without seeing the issue, it’s tough to diagnose the problem but I do have a couple of ideas.
If when mounting the fender, if you have to bend the back or front of the fender back or forward to get some holes to align, it may cause the flange to bend in or out.
If the fender is replacement, you may need to tweak it a bit by either enlarging some holes or bending the flange to to get a better fit.