Back to the original problem then: why do bubbles sometimes inexplicably appear in the floor after everything was otherwise looking fine?
One explanation is there may have been a heap of micro-bubbles you couldn’t see that joined up to form a large bubble. If that is the case, the obvious solution is to remove as many of these as possible before they get a chance to form something more visible. Unfortunately this isn’t always that easy.
Some will say that they can use spiked rollers. From my experience I’ve found spiked rollers to be effective with filled epoxy resins, e.g. a 2mm self-level floor, however not so effective with clear coats. Rather than pop the bubbles or bring them to the surface, the spikes tend to push them around instead or miss altogether. Others will tell you fine bubbles can be popped easily by putting a blow torch across the film. Not only is there doubts about the practicality of this method on large areas, it also carries safety risks and the flame can interfere with normal product behaviour.
In my opinion, a more frequent cause for the type of bubbles we’re talking about is the expansion of air in the slab. As the concrete heats up, air is forced through the pores and can be trapped in a freshly applied film. It’s the reason why I’m such a big fan of working in the afternoon when the slab is cooling rather than first thing in the morning.