Algodoo

I don't think that's caused by a "glitch". You adjusted the density and mass of the box so high that it became extremely heavy, and it just forced itself through the bottom of the container. The same thing would happen in real life. That is, if you place an extremely heavy object inside of a wimpy, thin box, the heavy object will burst right through the bottom of it.

Why did it bounce then?

That's a great question! I didn't think about that before, and I can only guess at what's going on. I think that it has something to do with the amount of TIME that the box is in contact with that horizontal piece of the container. The Algodoo physics probably makes it bounce when the contact time is real short, but when the bouncing gets reduced to a very short amount, it is in contact sufficiently long enough that the box flows right through the container which cannot support the extremely heavy box any longer.

Hey, I'm just giving this a wild guess, and I concede that you may be correct in assuming that this weird physics is caused by a glitch in the Matrix.