It is not so rare to see bubbles appear on epoxy coating. The size of bubbles varies a lot, from an inch in diameter to as small as pinhead. You can find them in groups or scaterred around the floor. A phenomenon calle "out gassin" is what causes this. And it happens when the epoxy begins to dry up. Because the temperature rises, air is hotter and it expands into a bubble under the epoxy coating.
Use application primer as a tool that can help to prevent bubbles. You should use a slower drill to mix the epoxy coating, and when you start to apply it, be sure there is no sunlight hitting directly on the surface you are working with.
Use medium roller if you already decided to use one. Use gentle and slow motions when you are applying your epoxy paint. Our epoxy garage paint will have less bubbles with this.
You can use rotary scrubber ans some sandpaper to remove all those bubbles on your epoxy floor. The first step is to roughen the area with some sandpaper. Then scrupulously clean the dust. Also use a solvent and a rag to clean the area. When you finish this, apply one more coating. Fisheyes is another type of bubbles that can occur. The silicone that remained on the surface is one of the reasons.
Use sandpaper of medium grit to clean this area in entirety. Take a rag that is dipped in solvent and clean the area with some pressure. After this a fresh coating may be applied.
Consider shot blasting or sand blasting the entire epoxy coating in case the bubbles are spread all over that floor. Use sand blaster to remove the epoxy coat from the area you are working on. Afterwards clean the problem area with acid. If the troublesome area is very small it can be treated in isolation. A new coating will have to be made after you repair the area in question.
Moisture is also a cause of bubbles in our epoxy flooring. To verify this break one of the blisters thus formed and see if there is any moisture inside.