Continuity mistake: After Mrs. Russo puts Justin and Max in the lair, she is wondering if she should put the big lock on the door or not. She decides not to and puts the lock down on the counter. Two shots later you see the lock is back on the door, but unlocked. You never see Mrs. Russo put the lock on the door.
Continuity mistake: When Harper makes all the apples fall down, there is one more left on the stand. When it switches to Alex and then switches back to the stand, there are no apples on it. In the next shot the one single apple has reappeared back on the stand, then disappears again in the next shot.
Answer: Honestly I've been confused too. Thought the ones going down went to Justin's bedroom or to the station. Then the ones out the door went maybe to an elevator to those stairs I guess. Then the one to the side went to the lair But the freezer also leads to the lair or a secret spot sometimes too.
I think the ones in the sub shop go right up to a hallway in front of the loft, then the ones in the lair go to the bedrooms upstairs. Now there's a way to get to the lair from the loft and I believe it would be past the kitchen down to the hallway where we don't really see except in like one episode. Now what confuses me the most is the lair because when Harper finds out you see Alex using magic to open it into the lair but in every other episode you open it and it's the lair.