One is that it stores a "play count", the number of times you've played a song, directly in that song file. So it's always re-writing the source file of the track in the library.
That would be only mildly irritating -- radically blowing up the size of system backups, for instance -- but for the fact that it routinely corrupts the new song file stream.
I see so much bit rot in my iTunes audio files -- and nowhere else -- that the stupidity of not simply keeping some small database of play count veers over into uselessness.
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The second complaint is that they decided that any file I had ripped from my CDs were pirated, and therefore would require an annual fee for me to keep. I understand that's a concession they agreed to from music industry in order to roll out their "iTunes Cloud" stuff.
But yes, I bought more than 400 CDs new and yes, I still have all of them, and indeed, I never loaned them out to anyone else (no one asked).
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After a while, I just set my iTunes audio files to read-only, and a to-do item from ten years ago is to go through and re-encode my physical CDs. Still haven't done that, yet.
Stopped using iTunes, instead. Still need to rip them discs...