It's totally irrational, of course, but people can hold grudges for reasons that have nothing to do with them personally, over events that happened years or even decades ago. Ever hear of the Hatfields and McCoys -- or the Capulets and Montagues?
We know Outpost four has been attacked, sir, so if we intercept Romulans now . . .
After a whole century, what will a Romulan ship look like, Mr. Stiles? I doubt they'll radio and identify themselves.
: You'll know, sir. They're painted like a giant bird of prey.
I had no idea that history was your specialty.
Family history. There was a Captain Stiles in the space service then. Two Commanders and several junior officers. All lost in that war, sir.
Their war, Mr. Stiles. Not yours. Don't forget it.
: Yes, sir.
Stiles' suspicion that there may be Romulan spies aboard, and especially his sudden distrust of Spock, does seem to come out of left field. It feels like a writer's excuse to throw in a comment about bigotry.