Unless you're looking for de novo motif models, one option is to use TOMTOM to rank MEME hits by nearness to published TF databases. That should clean things up considerably.
Unless you're looking for really long binding sites (dimers, say) you could also set the
-maxw parameter in MEME so that you're looking for sites that are less than 25nt long. Tuning other parameters may be of use.
Another option is to adjust your background, by removing sequences from repeat-masked regions.