As before, I post here because there isn't much traffic in the episodes threads.
There were several holes in the episode.
1) The throwaway characters, Graydon and Dickerson were both in corridors when they were attacked by the wraith queen. Yet later Sheppard saw one of them already dead sitting in the seat of the jumper.
2) There were about 2 hours until the self-destruct mechanism would activate in the wraith ship (which had evidently been sitting down there at the bottom of the sea for thousands of years). For McKay and Sheppard to get there in their suits in less than two hours seems miraculous because they were walking very slowly and it was about 1 kilometer from the station. This was never explained.
3) The wraith queen was on a drip sedative to keep her under control, but no one explained why or how they had a drip sedative in the station, and who the available doctor was (remember, no more Beckett).
4) No explanation of who runs Atlantis when both Elizabeth and Teyla are not there.
5) No explanation of the interaction of Teyla with the wraith that led the wraith to deactivate the self-destruct, or for that matter how the wraith (which lives on oxygen) was able to get there with no deep diving suit.

Speaking of throwaway characters, you can always figure out that specific characters who have never been seen before and are on a special mission with the main characters will end up dead during the episode.