An album I purchased on iTMS recently had a nasty clicking sound in one of the songs. Its was part of the intro track to an Opera, and really hits you in the ear each time you hear it unexpectedly.
I had only just got around to reporting the issue, but iTMS staff rejected the issue due to the timeliness of my report – about 3 months after the purchase. I wrote back advising that this was a “premium cost” iTunes Plus track, and there is still an issue with the track they are selling, no matter the time frame.