Sometimes the slag used in a concrete mix can cause such problems. Best mix contains limestone, but in some parts of the country, mill slag is used. For some reason, mill slag tends to come to the surface later. We have neighbors in our area of NE Ohio that have driveways that have so many popups that they have to sweep the slag off the surface, leaving a rough surface. When I built my last home, I had a blacktop drive set low and placed interlocking paver bricks on top of the black top. Pavers are made of high pressure concentration and seldom if ever give a problem. If a paver should fail, you just pull it up and replace it! Unfortunately such a driveway is very expensive but sure looks good!
For indoors, you do not often see concrete pop, but it can do so, especially in an unheated garage. I do a lot of construction and always specify at least a 6-sack or 6.5 sack mix and order it air entrained and pour it 6" in depth, along with rebar reinforcement. I also pay extra to add micro fibers to help hold it together. Some try to save money and buy 5-sack cement and in my opinion this is a bad move. I recommend paying a little more with a quality supplier when it comes to cement.
If you look closely at the pop-ups can you see any small stone (some times blue or black) or evidence of something like that? That might indicate mill slag or other impurities in the mix. Also, sometimes too much water is added when pouring the cement to get it to level out faster. This is also a bad move, as the cement will be stronger if excess water is not added. After the concrete is finished, we usually apply a liquid sealer to keep the surface smooth and clean.
Attached picture shows one of our buildings where the floor was sealed. We recently completed this 60' x 96' garage and added speed racks at one end for more storage. So far, have not yet finished organizing our warehouse, but will be doing so soon. We use a numbering system with metal signs around the perimeter of most of our buildings, and later develop an index (by location number) in alphabetical order. This helps us locate whatever is stored in our buildings.
My accountant once told me that "there is nothing like a clean and well-organized warehouse for proper inventory control". I find this to be very true.
Fred