From Encyclopizza
There’s a difference between bubbles
formed from under-proofing versus
over-proofing. Bubbles from
under-proofing tend to be flat but
large in diameter. If unpopped, they
can blow up an entire pizza. This is
the process by which pita or pocket
bread is made. Bubbles from
over-proofing tend to be high but
smaller in diameter. They rise up like
little ping-pong balls and eventually
form a hole at the top, at which time
they stop expanding. They almost
always burn. Most pizza bubbling
problems are of the under-proofed
type.
To resolve a bubbling problem, dough
fermentation must be adjusted
accordingly. To stop bubbling caused
by under-proofed dough, increase the
amount of fermentation. To stop
bubbling caused by over-proofed dough,
reduce the amount of fermentation.
In addition to proper proofing, it has
been found that reducing the amount of
water in a dough formula can help with
reducing bubbling when dealing with
the under-proofed type. The reduction
in moisture aids in creating the
pinpoint holes in the cells walls.
In addition, you want to make sure you properly knead your dough. Some people poke tiny holes in the dough to prevent overly large bubbles. As a final resort you could observe your pizza in the oven and poke bubbles as they form.