I had the same issue in my 12 when I first set it up, where th bubbles were isolated to one rock, but the count was growing.
I waited until a WC where the water level was low, then pulled that one rock out and took it to the sink.
I picked off the bubbles with a fork. Some came easily, some were connected to the rock with some kind of root.
I ended up popping two, so I washed off the rock a couple times with the waste water afterwards to remove any trace of spores.
That took care of it. Haven't seen a bubble since.