Square button? I'm sure it's triangle to strangle them... Could be wrong as I have had the same problems but with Clickers and runners.
Square: Strangle (or aggressive kill in combat)
I have acquired the grade of Master in The Last of Us story/character/game knowledge as I have played it through 9 times.
... I have no life.
I've never had this issue. Maybe it's because you're dragging the enemy into a room, which the game might consider a new area, and being the only enemy in that room, it assumed he's the last and goes for a loud kill. Problem is, I don't think this ever happens. My best guess is that you had been spotted before which caused Joel to commit an open combat kill.
Yup... I did say it only happened after a drag and stopping dragging has stopped the loud kills. I was trying to do what the game told you to do... I used to drag them out of possible sightlines before strangling so that the body isn't discovered right away..
But as others have said it has happened to them (although infrequently) shows that it DOES happen. It's an intermittent glitch I think. Like I said, if I click the Square to strangle I expect to strangle and not do a flashy kill.
I nearly strangled Ellie last night too... I went to strangle this one guy just as Ellie pushed between Joel and my target. There was Joel looking like he was strangling Ellie for about a couple of seconds before the target capped Joel because he had missed. Joel was stuck in the strangling animation while not having anything to strangle.
I must be cursed..... heh... Did give me a fit of the giggles when it happened though. Looked like Joel was peed off with Ellie because she blocked his attack.