When Mulder and Scully are examining the dead prostitute, you can see her eyes moving beneath her eyelids.
At about 33:30, Mulder and Scully ask Judy about the man who hired and killed Carina. Judy says she didn't really know him and never talked to him, but when Mulder asks her to call him with his phone, she dials the number, apparently from memory.
When Skinner visits Sharon in the hospital, you can see her blinking while she is supposed to be in a coma.