I haven't played yet but testing out the tower I threw in all the yellow cubes. They lined up on the second row along the walls . Then I threw in another color and its hard to knock off the yellow ones that are there especially in the corners. I even tried to throw them at them to knock them off and it didn't work. Anyone else notice this? Maybe I should remove the top row?
To be less snarky, there is an initial seeding, that is mixed up of all colors. those will catch in the places you're worried about.
You won't be throwing in a single color during the game so you aren't going to have this exact situation. Most of what goes in comes out in that same toss. But it will catch a couple and eventually knock some of those stuck ones out over the course of the game. That is where the randomization is going to take place. that is where the "upset" win can happen.
So don't take the top shelf out. It is doing what it is supposed to. It is probably just more pronounced since you used all of one color.