If you are not getting cut through and you have locked the position of the work so it cannot move you can run a second cut and it will be in exactly the same position as before, so where it did not cut, it should on the sequential cuts.
If you see flames instead of smoke, that interferes with the laser and it will not cut as deep there. If you head fan (behind the head) is at all slowed you are more likely to allow the smoke to catch flame.
There are many explanations on that as well…