I bet what Marshall sees on the computer screen is that someone from WITHIN APO is deleting the files that Marshall is trying to access. That is why he thinks "it can't be" someone that they work with - a friend of Sydney's - that would be sabotaging the files to find her.
Plus, if it is Sloane, then it wouldn't surprise Jack at all and that's why he says "its not wrong". Because, he knows, he just HAS to know, that Sloane isn't on the up & up. He asked him point blank this episode, so you gotta know that the wheels are turning in Jack's mind with Sloane. Things are not all as they seem.
I think there may be another mole/traitor at APO. The way that they showed the clip after Horizon, when they mention that "betrayals" will begin, we see Thomas hiding behind a wall just as a blonde (Rachel) walks by. Sooooo, is someone else behind this????? Maybe Thomas is related to Irina somehow (maybe that is what Jack saw in his file that "surprised" him) and now Jack is putting 2 & 2 together????
Oh my gosh, the possibilities are endless! I am so glad that S5 hasn't disappointed!