I think I'm having the same issue discussed here:
See below. I have holes in the assembly, scope to cut through a single part, and when finish the command, I get no holes. The larger hole between the two small holes is a different assembly hole feature and it does work.
Sometimes I get one hole, sometimes none. I tried using an assembly cut feature instead & got the same result.
Is this a documented bug? I haven't contacted my VAR yet - not looking forward to it after the last interaction.