The sentence you show could be correct in another context, but not in this one, which is reported elsewhere (with a slight and immaterial difference):
HANI: He was in the room because I put him there. I'm just sorry I wasn't there a few minutes sooner.
ROGER: Alright, what would have happened if you were a few minutes later, huh?
Clearly 'Roger' is posing a counterfactual contingency, 'Hani' arriving later than in fact he did; he implies that Hani arrived too late to prevent one sort of misfortune, but early enough to prevent another. You are therefore correct in believing that this should be expressed as if you had been a few minutes later.
You should realize, however, that in improvised speech (which this script emulates) neither speakers nor hearers are particularly attentive to these fine points of expression. Complex counterfactuals like this are relatively infrequent in ordinary speech, and most people don't use or hear them often enough to 'appropriate' them into their unconscious syntactic portfolios. Consequently, you are likely to hear exactly this sort of error very frequently. What Roger means is perfectly clear, and that's all that matters in casual speech.
The lessons to draw from this are
- You shouldn't expect improvised speech to be strictly grammatical.
- You shouldn't regard such errors as anything but casual and trivial.
- You shouldn't use informal speech as a model for your own English. Points 1. and 2. don't give you license to make the same errors yourself. Standards are more stringent in written academic contexts.