point discrepancy

[Putty]

Freshman tournament, I am T partner is L. Play occurs on his side. Girl shoots. I assume that it is a 3, because I see his arm go up as if to give prelim. signal. I give the "it's good signal" and head down court. I am not sure how much time went by, maybe 35 seconds, the table buzzes us over. The visiting coach wants and explanation on the shot. She swears that one of us gave a two signal and the other a three. As it turned out the L could not remember the shot or any part of the play. He said since there was doubt between the two of us we had to count it as a two. This after granting the shooting team three points on that particular shot. My question is did we handle it correctly.