YouTube officially discourage the upload of clips featuring copyrighted materials (video or song) to their site, unless the poster sought permission from the copyright holders or can claim that their particular use of a copyrighted video or song qualifies as a "fair use." Some info on YouTube's copyright policy can be found at
http://www.youtube.com/t/howto_copyright
In practice, YouTube will take clips down or ask posters to take clips down, only if a Digital Millennium Copyright Act (DMCA) complaints are filed (usually by copyright holders). Actually, DMCA complaints are not regularly filed, either because copyright holders are not aware of copyright infringements or because if their materials are not resulting in a profit for those who used them, they may see it as a some free publicity.
Anyway, your problem seem to be on just one of your clips, so I wouldn't worry about what to do with the others, and I would contact YouTube and try to clarify the matter with them.