You say that the machine isn’t in alignment. This is the cause of your gouging. As you sweep the stone on the lap you are putting the edges of the stone into the lap and cutting grooves. The solution is to align the machine.
Another option is to use a very small area of the lap and cut and polish in the same place (say at around 3’oclock) and use a very small sweep almost like scratching a lotto ticket. This should minimize the effect of the machine alignment.
Besides the alignment problem a similar thing can happen if you are off on the angle from cutting to polishing. Putting a sharp edge of the stone into the lap is sure to dig in through the diamond and cause grooves.
The good news is that groves typically won’t ruin the lap. People used to score laps after all.
A piece of synthetic corundum at least 1/2″ square is a useful tool for knocking down edges of gouges so they don’t cause problems. Just use the same process as is often recommended for initial charging and the lap should still be usable.