After the off-world team fires long bursts at the Iratus bugs, when they exit the cave, the P90s all have full magazines.
The container with the eggs was full to the top when he put the lid on and when it was opened it was not full.
A close-up of Sheppard's arm as he pokes the wounded area clearly shows that the area of the wound that's changed is a prosthetic.
When Ronon Dex first shoots Colonel Sheppard and stuns him you can clearly see his arm did not rise to make the first shot, hence the second shot he made was the only one he took.
John Sheppard is wearing a wedding ring during his sparring match with Teyla.