Ubisoft seems to have heard these concerns and worked double-time to get a patch out that fixed the biggest ones and says that the update will be out at the end of next week. There are said to be over a hundred fixes, spread out over the main story mission, side missions and the multiplayer.
I remember this one instance where we were supposed to shoot at some explosive barrels in a cart, but for some reason, my character refused to aim at them. It turns out the real explosive barrels were on the ground under the cart, but the icon made it confusing and wasted the better part of fifteen minutes of gameplay.
Thankfully Ubisoft is correcting this and many other problems both small and large. Note: the PC version will lauch without these issues. Here is the full changelog, but be wary of plot spoilers.