Christ, they can be infuriating.
I just spent like 50 mins playing through a couple of objectives in a mission in ACIV, taking my time, making note of enemy movements, trying to remain undetected, etc. Saw the game save under a rock arch around the halfway mark.
Completed the second objective of the pair, and received a third, to swing from a tower and air assassinate a dude.
Swung from the tower, let the guy get highlighted, pressed square.
Landed behind him.
But that's not the worst part, oh no: I reverted to the previous checkpoint, to... Maybe this new objective appearing? Under the rock arch? That would be too easy!
No, the game took me back the better part of an hour to the very beginning of these few objectives. -blam!- you, Ubisoft, and your -blam!-ing buggy 'next gen' engine.
[spoiler]Now pardon me while I consider Child of Light.[/spoiler]
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AC IV worked perfectly for me all but one time where there was a random graphical glitch (which resolved itself). I suppose there's no pattern to why it happens, you just have to be in the wrong spot at the wrong time.