There are many rooms where Background 2 (BG2) elements are completely covered by Background 1 (BG1) elements, so they've never seen during normal gameplay. There are also some cases where tiles seem incorrectly placed. These are most likely remnants of previous room designs, since we know from beta footage and screenshots that many of the rooms looked quite different. I was only able to find two beta screenshots that lined up with the hidden BG2 elements, but it's interesting to speculate on how the rooms were changed.

You can use the level editor MAGE to view any of the rooms and toggle the background layers.