It seemed like the refs early on decided they would not be throwing many flags, which is fine as long as it is consistent. While there could have been a PI call on that last play, I wouldn't call it obvious. As many have mentioned, the 49ers benefited greatly from the non-call when Flacco was clearly roughed the series prior. I think in the regular season that gets called 99 times out of 100.
Ultimately, I thought the Ravens played a better game beginning to end. They made less silly mistakes and deserved to win. The 49ers were the better team, but they made too many costly mistakes early on to deserve this win.