Entering the TF Mastery Screen updates the mastery information each time to make sure they are right. It could be that you just got barely enough mastery points after a run through some bonus like winning mastery. And because the game only checked again after you left that area you got it then.
That would be my guess since that is theoretically possible but ultra rare to actually happen.
I need to add all items manually to a removal list so I might overlooked them. Oh yeah it seems I forgot to add flash grenade DX to the remove list. With three potions I assume you mean the Purification Potions? I just saw they also were missing on that list. Will fix them thx!