One was the opening when Charlie gets the arrow in the neck. I was mainly thinking "this is a Desmond dream" but I have to give props to the show because just for a few seconds I thought "what if they really *do* kill off Charlie right here? That would be wild."
The second was one that many people might have missed. It was near the end, when Desmond goes to turn his "monk clothes" back into Brother Campbell. The camera did a slow pan over Brother Campbell's desk and showed a picture of the Brother with a woman. The quick of eye (or of Pause button) realized the woman was none other than "Ms. Hawking" the jewelry store owner from the previous Desmond "time travel" flashback episode. This was the woman who explained to Desmond, "no you don't buy the bracelet, you break up with Penny because you have to end up on the island and push the button." What the -?!?!
Damon and Carlton have stated, in podcasts, "Desmond did travel back in time in that episode" but then how does Ms. Hawking know what is supposed to happen. I'd feel better if they just attributed it to a dream/hallucination of Desmond's. Items like this are when I worry about how LOST is going to resolve things like this. Using either "time travel" or "multiple universes" as an explanation for everything is just too much of a cop-out as far as I'm concerned. This is one of the reasons I've never been fond of time travel or multiple universes in speculative fiction; it's just too easy to have everything conveniently work out or conversely, to have anything happen that you want.