During the quest 'Phase 1' for the Underpants Gnomes in Stick of Truth, I have definitely collected all five pairs of underpants, but my quest journal has only logged four pairs!? Quest items cannot be sold, so I can't have lost them... Any ideas?
A friend of mine had a similar issue. He was in day 2, and got too many friends. The game automatically forwarded him to day 3 without going through the proper quests.
I believe this is similar to what you are experiencing. If you get to a certain point in the game with too many friends, items or whatever, it "shoots you forward" without counting anything properly.
Unfortunately for my friend, he was missing a key item to advance in the story. As for you, you just miss out on 1 friend (an achievement in this case).