Sorry about the language there.
The early leader in the clubhouse as far as Cosmic Encounter rules confusion appears to revolve around a player's second encounter, and, more specifically, what happens if the offense runs out of Encounter cards (including from not even having any when the encounter begins)?
The rules actually spell this out (see pages 7 and 13 of the Fantasy Flight Games rulebook), but it is certainly a bit counter-intuitive, especially considering earlier editions of the game handled the situation differently. And there's definitely some confusion out there, so I wouldn't be at all surprised to see a second-encounter example end up in the FAQ, which, according to rumor, is due out fairly soon.
Meanwhile, here's a sampling of some of the discussion:
A forums thread;
And a third thread.