The question is, are these areas expanding?
This is a relatively new pour. If you only have a few area that are stable and not getting worse, as Scotty recommended, you can grind and re-float them prior to painting. If the floor is slowly abrading in multiple areas, the whole pour is suspect.
If these areas are isolated and not degrading further, then a repair is a viable option. One of those looks like a tool may have been dropped into the mix later in the working process and filled in with loose creme. That creme may have been watered down and has little strength, hence the decay in the surface with traffic.
To know for sure, get a pressure washer and hit the damage. If it grows and then stops, try other areas that appear undamaged. If there are more, I would treat the pour as suspect. If your areas grow by 50% and then the decay under water pressure stops, you probably have some surface anomalies that can be ground and filled prior to painting.
Either way, you need to find out and a 3000+ psi pressure washer is a great way to check the concrete condition. Plus, if your aim is to epoxy coat anyway, you will have removed the creme dust if you do the whole floor. Takes awhile but, with a roller work seat, you can get a lot done in an afternoon.
Should you find the washer pulling up more and more areas of decay, definitely get the contractor and supplier involved, if you know who they were.
Ray