From what you describe, and if there was indeed lignite in the concrete, it sounds like the problem stems from the fine aggregate (sand) used to make the concrete.
Lignite is sometimes found in natural sand. The amount varies, depending on the quarry and the particular deposit. When sand containing lignite is used to make concrete, lignite particles near the surface can expand and cause the popouts you describe. At first, you'll be able to see the small, dark lignite remaining at the bottom of the popouts. But because it is relatively soft, it will soon wash away.
There is a standard limiting the amount of acceptable lignite in the fine aggregate, ASTM C 33, "Standard Specification for Concrete Aggregates." It addresses both strength concerns and the concrete's fitness for purpose, which includes appearance issues. Although the standard allows up to 0.5% "coal and lignite" (for pavements), it permits a higher percentage if the strength is not adversely affected and some other non-expansive criteria are met (under "Deleterious Substances," section 7.3.)
How you deal with this problem depends on how unsightly you find the finished product. If you have one popout per square foot, it might not be worth pressing the issue. But a dozen might be worth the aggravation you’ll encounter if you have the contractor or producer remove and replace the concrete. If you pursue that, you might want to find a consulting engineer who specializes in concrete.
The strength of the slab should not be adversely affected. Applying a sealer may help keep additional water from getting in and expanding any more of the lignite. Choose an acrylic sealer that has good moisture vapor transmission quality.