From what you write I understand you have recoated part or all of your floors?
Have you only treated part of the floors, or you have coated entire area? Blisters, may usually appear when:
- Coating is done directly onto old finish without good clean of the surface and without using Bona Crosslinker - when recoating wooden floors at least buffing with a light screen is recommend prior to application
- Previous coats and new coats are not compatible - Bona is a waterbased product, was the previos finish waterbased? or compatible one?
This is basically a coat, which has poor bond with the finish below. Unfortunately, I cannot think of an easy way of rectifying this without proper floor sanding and refinishing.