Slater,
There are several possible culprits. But first, are you using a true phenolic backed veneer or a polyback veneer? The latter is a resin impregnated paper that is more flexible than a phenolic and a lot less brittle. A true phenolic is a little more challenging to fix.
Make sure your bending ply is sound and smooth. Also make sure that your glue application is as smooth as possible and that you are getting complete glue coverage. When applying the veneer make sure you use a scraper or veneer hammer to apply as much pressure as possible. Stay away form J rollers, they will not give you enough pressure.
The bubbles are caused either by not enough glue in those spots or the glue was didn't flash off all the way before the two surfaces were mated. So the off gassing causes the bubbles.
If there is not enough glue in the joint then you might have to inject some into the bubble and flatten it with the scraper and/ or a warm iron.
If there it is caused by solvent gases then you might have to make a small incision going with the grain to relieve the pressure. Make sure you go through the phenolic/ polyback backer. Once you have relieved the pressure you can use your veneer scraper and/ or a warm iron to set the glue.
The other problem (and this is the least likely scenario) might be that the bubble is between the veneer face and the backer. This happens but very rarely and the only way to determine that would be to cut all the way through the bubble and see where the separation is occurring. This is not always an option if you are trying to save the project. try the steps above before you start cutting things apart.