It's totally irrational, of course, but people can hold grudges for reasons that have nothing to do with them personally. Ever hear of the Hatfields and McCoys -- or the Capulets and Montagues?
STILES: We know Outpost four has been attacked, , so if we intercept Romulans now . . .
KIRK: After a whole century, what will a Romulan ship look like, Mr. Stiles? I doubt they'll radio and identify themselves.
STILES: You'll know, sir. They're painted like a giant bird of prey.
KIRK: I had no idea that history was your specialty.
STILES: Family history. There was a Captain Stiles in the space service then. Two Commanders and several junior officers. All lost in that war, sir.
KIRK: Their war, Mr. Stiles. Not yours. Don't forget it.
STILES: 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.
The Hatfield-McCoy was a series of conflicts and murders over not quite thirty years. There's certainly no hostility at that kind of level between them today, over 120 years later. (Members of each family competed on "Family Feud" in the 70's and thousands of descendants socialized at a massive reunion in 2000).
The Montagues and Capulets, of course, were fictional. We never learn what caused their conflict or how long it had been going on anyway.