I really don't like how much faster vortigaunts shoot in BM. They were slower in HL1 so you could have time to get out of the way of their attack, because there's no real way to dodge it.
There's one bit in the BM version Surface Tension where you drop down a hole, and there are two vortigaunts already waiting to jump you. There's no cover and there's pretty much no way to avoid getting damaged without knowing that they'll be there ahead of time. Stuff like this is on the same level as the imp doors from Doom 3 when it comes to cheap enemy placement.
If thats the part I am thinking about, you can get past it without getting hit. The second you land sprint at them and shotgun them both in the face. They usually can't react in time.