At the start of the church song, the janitor can be seen in the background, already clapping to the rhythm. About ten seconds in, he is shown still, then he starts clapping, as if drawn into the music.
When JD's comatose patient awakens, his endotracheal tube ( which is suction tubing and not an airway tube-look for the white collar near the mouth) is not secured in any manner, with the exception of the patient biting on it.
JD's comatose patient is intubated, but also has a nasal cannula on. Endotracheal intubation bypasses the naso/oropharynx delivering air directly into the lower airways making nasal oxygen unnecessary.
After his on-call shift, Turk comes home wearing a blood covered scrubs top. No doctor would ever leave the hospital wearing contaminated clothing.