The action in this episode takes place prior to the United States' entry into World War II; the analogue to Scully claims to be working for the Office of Strategic Services (OSS), but that agency did not come into being until 13 June 1942, about six months after the US entered the conflict. However, since the WW2 era sequences are as likely to be a hallucination as time travel, this may be deliberate and based upon Mulder's lack of knowledge.
When Mulder has stolen the parallel Spender's uniform, an SS Untersturmfuehrer's (junior lieutenant's) one, and is trying to sneak away, a lower rank German soldier (probably a petty officer) asks him if he found something. He uses the informal pronoun "du", inconceivable by a subaltern especially in Nazi army, instead of formal "Sie". Instead of "Hast du was gefunden?", he should have said "Haben Sie was gefunden?". However, since the WW2 era sequences are as likely to be a hallucination as time travel, this may be deliberate and based upon Mulder's lack of knowledge.
Mulder says "I don't speak Nazi", instead of saying "I don't speak German." Of course, he's intentionally insulting the person he's addressing.
Around 00:44:05, we can see the mic's shadow on the wall, just on top of Mulder's head.
The first time Mulder points out the Bermuda Triangle on a map (Bermuda-Puerto Rico-Florida), he points to Cuba and not Puerto Rico.
SS and Gestapo uniformed soldiers would highly be unlikely to board a ship at sea, German Navy or Kriegsmarine would be the ones. Probably those uniforms or duplicates were unavailable.