Dealt with this years ago, but it's come up again for a friend on Avid 8.x.x so I figured I'd write it out. This is so stupid. When you AMA link clips, avid generates a pointer hash that tells the bin which clip file is being referenced. Unfortunately, whatever algorithm generates this hash is totally stupid and frequently creates duplicate hashes. The result is that clip AH010602A01.04 suddenly has a tape source of AH010602F03. Fucking Avid.
It doesn't matter if the clips are different lengths, have different TCs, or are even in the same format. If you have AMA linked clips, you can have bad reference pointers. The problem isn't super common (maybe 1 clip in every 50), but if you're working on a real show, it'll pop up daily. Yes, before you ask, dear reader, this will happen with quick ingest XDCam stations since they AMA link to the MPEG reference files for copyover.
So how do you prevent this nonsense?
Well, you can't. Not really. The best I've got is a shitty workaround that adds a fuckload of time to your already busy schedule, and it fucks you if you're trying to do a true tapeless workflow (well, it fucks online, not you, but you shouldn't be going tapeless anyway).
The short option is to transcode full-res source files to Avid codecs and edit in full res. That's the only tapeless solution I'm aware of, but it's going to take up a fuckton of storage space. Don't go tapeless. Ever. One magnet or power surge or misplaced glass of water will make you lose your entire fucking show.
The longer, shittier option is to output those full res clips to new master tapes and capture them normally, or AMA link the master tape clips and then transcode the AMA link files to low res media for edit (which can be properly upressed for online later). God forbid you just transcode the full-res files to low res Avid codec media for edit, when you get to online you'll need the entire master files (and a correspondingly large amount of media storage) in order to upres.
It's a fucking shitshow with AMA links as your primary media extraction tool right now. I had hoped they had fixed this in 8.x.x but word on the street is that it's still a big problem.
If anyone still reads this shithole blog, please let me know if you find a more elegant solution! Thanks everyone. Except you, Avid; you're a steaming pile of hot garbage.