Don, was the floor warm when you laid the vinyl on it? There are temparture constraints for using vinyl adhesive, and they should be listed on the can in the directions. It's usually something like 55-65+ degrees at the time the floor is laid, and then continuously for about 48 hours after that. Read your product and you'll get the specific answer. And remember, they're talking about the temperature at the floor level, so if it's 65 degrees in the room, it's colder at the floor level.
The other thing might be either missing patches of glue, or not using the appropriate tooth depth when you combed out the adhesive. Perhaps there was not enough glue in those bubbled areas. And did you let the glue stand open on the floor for the 10-20 minutes usually recommended before you put the vinyl down over it?
I don't know how large an area you have a problem with (if it happened to me, it would be HUGE and undoubtedly located smack in the middle of the floor!), but you can try injecting the adhesive through the vinyl and underneath the bubbles with a hypodermic tool. Needless to say, it's a mighty messy business loading the hypodermic, but might be worth a try for you. If you're very careful with the hypodermic, the puncture holes will be small, and can be filled with clear vinyl patch you can purchase at flooring stores (I think David recommended clear nail polish to another reader earlier, so check past posts for vinyl floors). Best of luck.