When Mulder is looking through papers in Gauthier's apartment, he picks up an envelope. The name on this envelope when he picks it up is Marcel Gauthier, but when it is shown in close-up next to another piece of paper, the name changes to Bernard Gauthier.
Scully makes a comment while reading test results about how the man had increased leukocytes and was therefore healthy. Having increased leukocytes is a marker for infection, not an indicator of immune system strength. As a doctor, Scully should have known that.
Scully goes onto Miramar NAS to visit/question a Naval CMDR about the P-51. She tells him she used to live next door. She states he was a pilot in WWII and he would therefore be well past retirement age. Military retirees are not provided base housing. The CMDR would not have been allowed to remain in his active duty housing after retirement.
While the Piper Maru is supposed to be a French ship and the French secret services are involved, only background voices have a French accent and no accurate accent is actually seen spoken on-screen ; all on-screen "French" characters have at best Canadian accents.
Mulder handcuffs the female suspect using the wrong arm. He handcuffs her across HIS body which while it allows for a later scene where he's closed inside an office away from her makes no practical sense.
In the beginning, when they are using the crane to lower the dive suit into the water, there is a brief view of the land mass behind the ship; the ship is supposedly to be in deep water.