With a relatively large assembly, sometimes solver does not exactly calculate the placements (I suppose), so a face is left after the Cut operation. Think that we want to subtract the red one from the big one:

If the red shape's height is a little bit smaller than the big one (big: 10mm, small: 10mm - 0.00001mm) we still see the height of the red part as "10.00 mm" (not ~10.00 mm), and there is a little piece is left after the Cut operation:

How can we define a tolerance so that we could remove the face for that amount of differences?