The Doom in the Boom - S11-E10
Plot hole: Dr. Vizeri leaves the Jeffersonian months prior to this episode (confirmed in the episode) however, after turning up unannounced he still has his work jacket. It is unlikely his jacket would still be there. (00:20:05)
Suggested correction: It is not unreasonable to assume it was simply put into storage rather than being thrown away. It was perfectly usable and could have been used by another member of staff if theirs was unavailable.
I've forgotten the exact circumstances of Dr. Vizeri's departure, but the Jeffersonian probably would not have a policy that required personalized work clothing to be returned. Dr. Vizeri indicates in the episode that it had been his strong desire to return ever since his departure, so it is likely that he would have retained the garment for practical, or at least sentimental reasons.
The Secret in the Service - S11-E17
Plot hole: The chute is supposed to be so narrow that it injured the Secret Service agent's shoulder, but is wide enough for Hodgins to fit down comfortably in a sitting position.