Bubbles are often caused by the edges of the layers sealing before the air can escape from between. This frequently happens in side fired kilns, and top and side fired kilns.
Set up heat baffles around the edges of the sheets being fused to decrease the chance of the edges getting more heat than the centre and trapping air between layers. The baffles can be made from kiln furniture, strips of fibre board, cut pieces of old kiln shelves, etc. - anything that will witstand the top temperature.
Arrangement of glass sheets
Designing for fewer bubbles
Edge supports to reduce bubbles