You have to take your one pressure compensator and upgrade it in the modification station (not the moonpool, vehicle, one) to Mk 2 then Mk 3 to get deeper and deeper. They no longer stack, all you need is one and the Mk it is at.
Don't feel bad as I made the very same mistake. The issue now is there is no way to break apart the extra upgrade modules for resources after you have built them. Maybe this is something they will add in later.
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