Here's a thread to nominate those tracks that are almost perfect but let down by one element. Here's a couple to kick off.
Labi Siffre's gorgeous "Something Inside So Strong" has an instrumental break that should be played on a saxophone, Baker Street-style. But, being the mid-80s, it's played on a synthesizer which, unfortunately, sounds like a saxophone farting. Fail
Before recording the bombastic, Clapton-fuelled version of "While My Guitar Gently Weeps" that appears on the White Album, George Harrison recorded an acoustic version, with only a few bars or organ accompaniment, played by McCartney. This is available on the Anthology box set and is exquisite... apart from when George inexplicably chooses to pronounce the word "alerted" (as in "no one alerted you") in an exaggerated Scouse accent, extending the 'e'. It sounds awful and spoils an otherwise perfect performance.
Any more?