1968 and 1976 were very close despite anti-incumbent years.
Reagan was fairly, but not "massively" popular during the 1988 election year.
2000 was pretty pro-incumbent, but ended up being ridiculously close. I wonder if Gore were a little more exciting, would he have had a mildly comfortable victory?
Yes, Gore in 2000 is the most obvious case of a candidate underperforming the fundamentals. 1976 being close was consistent with the economy of the time, but when you add in Watergate, I agree it's surprising Carter didn't do better and that should have been a warning sign for him. 1968 is a case of a very good economy with an incredibly unpopular war at the same time, so I guess they basically cancelled out. It also wasn't nearly as close in the electoral college. It also looks like Obama underperformed the fundamentals in 2008 on the surface, but that might just be both parties now having higher floors.
Some people would say Obama overperformed in 2008 because of the economic meltdown. My guess is that he would've won anyway, but I think the huge economic downturn made certain states closer, plus wins in Florida, North Carolina and Indiana.