My sympathy... I had the same problem with a couple of early bows. They tended to be at the edges and I was able to grind them off as I shaped the bow. Don't know of any actual fix for the bubbles themselves.
Some thoughts..
I've been watching because of interest in the caul. I'm very suspicious of its ability to apply pressure evenly. Purely a gut reaction, no real experience with the concept. I put my confidence in a heavy metal bar, one piece full length and pre-bent to accommodate the riser. Not fool proof, still get the occasional tiny bubble, but seems to always be out at the edge. Had a couple on the bow I just finished yesterday, but again, they were ground away in the shaping.
My bubbles tended to be at the fades, where it's really hard to get even pressure. (Talking Hill styles) I don't use an absolutely traditional riser. I kind of redesigned it into a pattern with much gentler curves and I don't break the back glass for the layup. I use the full 6' piece, then grind the back riser flat off the finished blank.
I went to adding a 1 1/2" wood foot to each clamp; so that instead of a round pressure point, I had a square the width of the back brace strip.
I keep the wood warm in the oven at 90 degrees while laying up on the theory that it helps the glue to spread evenly.
Pre-warm the glue, see above.
A few tiny bubbles are annoying but survivable. Use judgement as to whether what you're looking at is going to cause weakness.
Scary thought for the day: with opaque glass, the bubbles can still be there, you just don't know it...