I had the same experience with my first epoxy product.
The problem with areas of poor adhesion indicate there may be areas of concrete creme that were not removed prior to the first application. Creme is the "creamy" mix that concrete workers work to the surface to give the concrete a smooth textured surface. Problem is, if the concrete starts to set up before they get it fully worked, they will add water to the surface. This so emulsifies the concrete that the creme has no structural integrity. It's like hard mud and will turn to dust if you scratch it.
WARNING: TO ANYONE CONSIDERING APPLICATION OF ANY PRODUCT TO BARE CONCRETE, ESPECIALLY NEW CONCRETE, CHECK FOR LOOSE CREME. USE A HEAVY WIRE BRUSH ON YOUR SURFACE IN SEVERAL SPOTS. IF YOU BREAK ANY POWDER-LIKE MATERIAL AWAY FROM THE SURFACE, THIS CREME WILL PREVENT ADHESION OF EVEN THE VERY BEST PRODUCTS.
This concrete creme is what produces concrete "dust" as it breaks loose under initial use.
My garage slab was poured on the 1st of July when it was 119F with a ten mile an hour wind -absolutely the very worst conditions possible. They had to wet the material down as they worked it.
My first application of another brand of epoxy simply covered up the creme. I pressure washed off the paint, and acid washed the remainder. Then, I carefully neutralized the surface with baking soda afterwards. The creme released and my second coat of Rustoleum bonded very well. The small patches of paint that held on stayed on after the re-coat.
Another caution. Acid washing of your floor may put tools at risk of rusting under acid fumes. Don't ask me how I know!
For folks trying to go cheap and easy putting down the Rustoleum or similar products: PREPARATION IS EVERYTHING! If you screw that up your life will be made immeasurably harder as I and many who post here about their experiences will attest.
Lots of guys get off to a start with only part of the picture. Like those in the old days who acid washed but never neutralized. Their paint started "bubbling" off in a week or so. There is a wealth of knowledge on this forum. Once you figure out WHAT you want to put down, make sure you figure out exactly HOW the process unfolds and follow those steps to the letter. Err on the side of caution. Cutting corners puts the whole job at risk.
Sorry for the "rant" but people contemplating do-it-yourself projects need to understand you can create a whole bunch of problems in a hurry that may take months to resolve.