I think it's amazing that it works as well as it does, but the issue is that when it doesn't work, it's really annoying. I could say, "Well, 98% of the time, it works every time." The thing is, when you settle into an album or listening experience, the point is to enjoy the music. When you suddenly hear something that isn't right, like a horn blast instead of a cuss word, or screaming fans instead of a studio track, it ruins the experience. I personally dislike most live recordings of songs. I'd rather be at the concert, thanks.
Some have had clean versions replaced with explicit versions. I don't have any clean versions of songs, so I won't have that problem, but that would really suck for say a mother and her kids, or maybe you're jamming at a work party and the boss is super-anti-profanity or something. When these problems happen, it can be pretty embarrassing, even only once in a million tracks.
I don't know how iTunes Match determines which tracks to match when there are multiple versions, but the fact that a live track can be replaced with a studio track means it's not solely based on the sonic fingerprint. It's been reported that sometimes it can mismatch if the track is a second longer than the version on iTunes, and cutting off one second can fix it. Whatever magic mojo they use to identify tracks, it's not perfect, and as long as that is the case, it will give plenty of people a poor experience. I find a messed up track either every time or every other time I play music on my iPhone, and that is way too often for me. In the meantime, I have resorted to just using my iPod or my Android, which has my tracks streaming from Audiogalaxy. So far, they haven't messed up yet, knock on wood.