The boat hijack level broke after using the on-boat ballista against the invading defenders. I scoured the level looking for what was no doubt the final invader who must have clipped into oblivion. I had to reload the entire level from the start to prevent this from happening.
Similar issue after retrieving returning the item to the ruined area in the Temple of the Spider. Two goblin-esque creatures are supposed to appear, which you have to fight before the gate will open. They did not, had to restart the level. The cliffside area had issues with the elevator (had to keep messing with the switch). Those are the major scripting issues; other issues involving enemy behavior are prevalent.
The game is extremely linear unless the final levels somehow open up significantly. What little exploration exists is akin to Uncharted 3 or Metro 2033, in that a quick deviation will get you a bit of treasure, and every now and then a combat zone will provide a couple different directions to kick enemies in. When I think of exploration that "matters" in a first-person non-RPG I think of System Shock (the first one in particular) or Realms of the Haunting. Really, the only game that Arkane has ever made that I think emphasized exploration in any meaningful way was Arx Fatalis, and that came out a decade ago.