Desmond was hit with the shot. If you notice when he's beating on Ben he only uses his left arm. The tell Desmond I'm sorry line was wierd. Maybe he's sorry for shooting him?
As far as the rest of the season goes from the spoilers I have seen two major things happen. The time traveling losties make it back to current time, and the incident occurs. I also caught the idea that dead is dead. Ben tells someone that and I think that is why he is so shocked that Lock is alive. His character is so complex. He cannot kill Alex as a baby when Widmore tells him to but he has no problem killing lock, or Ceasar for that matter. Just a "looking for this?" and boom, dead Ceasar. Ben not knowing certain things and looking confused was classic. I think the reason for the lack of judgement by smokie that some are complaining about, sort of makes sense. As evil as Ben has been based on our opinions I think that in the eyes of the monster those things were done to protect the island so he got a pass on all that. In otherwords we can't judge his actions based on societal norms but rather from the perspective of what the island thinks is correct in order to protect itself and it's secrets.
The island as a living, thinking being is really being brought forth this season. In past seasons it was hinted at and talked about, but this season they are actually showing examples of it acting out in a way to suggest that it does have a lot of human feelings like security, self preservation, and fear. Lock has had that sense every since he awake from the crash and could walk again. I think that even though we have not seen her this season much, Rose has the same understanding and I could see her becoming a large part of the story again because of her understanding of the island.
"What's past, is past"
but alot of times I think they just don't ask because the Island does what it wants and none of it makes sense anyway 
