Granted she was under pressure, but Simmons said some fairly unkind things to Fitz. Was that kiss one of adoration, of gratitude, or of affection? Was she really excited by being rescued by Grant more than she'd let on to Fitz? And, which is currently the main question in my mind on this issue, will Fitz become a villain, especially if he gets jilted?
One thing Wheadon likes to do is place characters in a series that are fated to be killed or turn out not to be as "good" as we think they are. I got the impression from this scene that maybe Fitz is the mole we thought Skye was.
EDIT: I just looked up LMDs on Wikipedia, and it says they are outwardly indistinguishable from the original, but any invasive procedures or am EMP pulse will expose them. It also says that they're controlled by the person that they're mimicing. I don't if that would totally eliminate it as a possibility, since the TV show can change things in any way they want, but it does make it seem a little less likely to me.
I really think that the suggestions are decoys. I think that something happened to Coulson that is "out of the ordinary" but that he's not an artificial lifeform. (In fact, I see no reason the original Torch can't appear in an episode as long as his name is not used.) I think that there is something else--perhaps he is immortal, for example.