Well the area waves are pretty much what I'm talking about. They often comes from areas you've already cleared which is a huge immersion breaker. The second story of the hotel (ie the area immediately after the E3 demo part) had guys coming up the stairs as part of the second wave even though the downstairs was entirely clear.
The only time it really bugs me though is that sometimes Joel will do a "loud kill" after grabbing the last guy in the area even if you've been entirely stealth up till then, and then that can trigger the "you got spotted" wave.
I have only gotten him to do that if it's the last enemy in the area and it never triggered me to get spotted.