My impression of Kyle was his bursts were based upon his feelings at the time. For the first doctor and the first time with Mulder, he was crying out for help. The second time against Mulder was when he sensed his adopted mother was feeling threatened and lashed out against him. Against dear old dad, it was anger and combined with his sister, the two of them apparently popped his brains out.
Perhaps I heard it wrong, but at the end, did they say dad's body was not there? Why would the siblings take it, especially if they caused the damage Mulder said he saw?
I agree with others here and feel everything is on such a fast pace it does feel rushed. Granted time is moving, but Sunday's episode presented Mulder's office as a shell while today it is fully operational as if he's been working there for weeks now. Perhaps there have been other moments happening - otherX-Files- but we're only getting a bit here and there overall. *shrugs*
The "what if" flashbacks with their child was a bit odd, since it seemed in that time their clothes and hair styles would not have changed.