Amazing Spider-Man Annual #36: What's wrong with Pete's memories?
For the record, I can't take credit for noticing this--Zarius on the SpidermanCrawlSpace messageboard found it.
In the latest ASM Annual, there's a scene where some new character wants revenge on 'Ben Reilly' for killing his family. Ben's name brings back memories to Pete, and we get this montage of poorly scanned panels and covers from the Clone Saga. Here's one of them:
Here's the source, from Spider-Man: The Lost Years #2...
So in other words...when Pete thinks he's remembering him and MJ, he's in fact remembering Ben Reilly and Janine.
Hardly the end of the world, but at the same time, I don't see how anyone could look at the original issue (and they had to to get the pic) and think that they're Pete and MJ. Unless they just skimmed through all the Clone Saga issues and just pasted on the pictures that seemed appropriate, which is what they were probably doing.