Dealing with ads blocking application functionality on iPad
If this problem happens in an App than your only chance is tell the developer of the app that the ad placement was a really bad user interface choice and to please fix this issue.

If you can provide screenshots and a brief description of when this happens (if it only happens under certain circumstances) they will most probably be very grateful and fix this problem ASAP.

Just as a precaution: be polite in your email and try to be as objective as possible when telling about your problem.