How often do you disturb the substrate? Sometimes gas build up in it from decomposition, which if left undisturbed eventually bubbles up very slowly.
The only other thing I can think of is you didn't let de-chlorinate, and the bubbles are from that. But that usually dissipates within 24 hours, and is only very small bubbles.
It gets disturbed pretty regularly, whenever I do a water change so usually every five to seven days depending on parameters. Although it's barely an inch of sand and I vacuum waste regularly so I wasn't too worried about decomp...should I be?
About the other option, I always treat with prime instead of letting the water sit and gas off because the water where I live is somewhat terrible.