I forgot to mention a few. There is a weird audio "glitch" at the start of "Never Learn Not To Love". It happens on the word "cease". It's on the old out of print cd version, and on the "twofer". The same thing happens during the first verse of "Good Vibrations".
Oh yeah, the two dropouts in the first few seconds of GV. I understand it had something to do with some rough edit splices, which is hard to understand with all the time and care that went into producing that masterpiece!
Here's one that gets me every time: a split second before the occapella section of "I Can Hear Music" there is a very noticeable blip. Perhaps an editing issue? There is a similar blip when the vocals come in after the instrumental break of the song "Friends", right around the time the clarinet (or whatever it is) hits that awkward note.