One where you have to retrieve the knive from the temple. So even though you have to fight through all these enemies who have their base there for no reason, then have to use your magical 3-part compass (which conveniently allowed for extra missions earlier in the game) to open a door and do some more Indiana Jones/Prince of Persia routines. But after you finally get the knife, it's almost a straight line to the open air.
The other one is one of the early missions on the southern islands: stealing a uniform from one of the rookie privates. After quite a lot of sneaking around, I finally find the one guy I am supposed to kill and strip (keep in mind that he is dressed and looks exactly like the couple of thousand clones you already killed). He's on a boat. And as it turns out, you can just SWIM AWAY after the mission. Which means that all that sneaking could've been avoided if that German contact person had bothered to tell you how to get away from that boat AT THE START.