(Around 15 minutes) Mulder is holding his phone vertically when he takes a photo of Chucky's hangman wall but in the next shot he is holding it horizontally.
At approximately 25:10, the waitresses name tag changes from saying Lisa (close up clips) and Sally (farther away clips)
Typically, a prisoner would have to surrender both belt and shoelaces when being locked up, precisely to prevent suicide attempts.
When walking round the psychiatric unit, Mulder asks Dr Russel about a patient, whom she identifies as Judy. Dr Russel says Judy is a schizophrenic and cautions Mulder against speaking to her because she has split personality. Contrary to popular belief, schizophrenia does not manifest as a 'split personality'. If Judy does have a 'split personality' a diagnosis of Dissociative Identity Disorder would be more appropriate.
When Scully confronts Little Judy's nurses about mysterious pills they may be giving her, she drops one of the pills on the floor without noticing.