Most video game glitches and bugs make it pretty clear they're a bug. You'll get flashing colours, or breaking objects, that sort of stuff. This Assassin's Creed IV hiccup, on the other hand, could be a bug. Or...it could also be the end of days.
Also, don't let that gif fool you into thinking the entrance to Davy Jones' Locker is all it does. Stick with it. It just gets better.