Reason why this can happen....
A composer's work can change licensing terms, status and rights can change if he sells out or changes label, management or later on signs with a 3rd party agency to collect royalties. Indie artists especially are always looking to get signed. That is why I strongly advise against using music from Bandcamp and Soundcloud. They are most not royalty free as well.
Best to look out for music directly from the composer that confirms that the music will be fully monetizable on YouTube instead of music that is within large collections where the composers are almost nameless and faceless.
A great place to start is of course Incompetech, Josh Woodward, Audionautixs.
My music is fully monetizable as well and I have over 5000+ tracks.
Jay, while you are at it, please don't confuse "large collections where the composers are almost nameless and faceless" with commercial Royalty-Free Libraries. While the music in these large collection isn't free (licensing fees must be paid), quite a few of these do one or more of the following to guarantee non-interference from the YouTube Content ID System.
A: Exclusive track licensing contracts; meaning that for the duration of such a contract, no other major distributor has the right to hold a copy of the tracks in another library. Such a distributor may also place their artists' tracks for personal (listening only) commercial distribution at such places as iTunes.
B: If a Content ID match is generated and cannot be successfully disputed, the artist who submitted the track is penalized by all monies generated by such music returned to the licensors, and the artist himself banned from the library.
While I don't have the size collection you do, my music has both the above stipulations attached; I am distributed by a major RF library out of Norway.