Finished a large Part of my Project which i need for my Masterthesis. I feel very relieved.

Are you still having this problem? I would definitely not stick anything over it without fixing the problem first. You could remove the surface rust with a CSD disc and treat deep-seated rust with a rust converter. If it’s only small and there’s still enough metal there, you would need to use a good rust-proofing paint. I use Owatrol oil and Brantho Korrux 3in1. It’s best to remove the side panels in the interior and see if there is any rust visible from above. Otherwise, you should definitely weld in a new part.