Problem with flags

Did you seal the bottom of the paving slab first ? Some are more porous and should be sealed. Check with the supplier. It might tone down when the cement is fully dryed out.

My first question would be was it laid by a marshalls registered contractor. If so it should be covered by their guarantee. Second were the slabs laid on a full bed of mortar and the backs of the slabs washed with a PVA/cement wash or equivalent. Third were the slabs up to British standard. A lot of cheap Indian sandstone is porous and can become susceptible to algae. Jcr Contracts. Home and garden

It will probably be alright for now, the dry slab has "wicked" out the moisture from the mortar, it's not the end of the world, but the cement in the mortar needs water to cure (go off), also, assuming you've dot and dabbed the flags, where the mortar touches the flags, this has more than likely NOT bonded to the flag, so quite possibly in the future the flags will "Rattle" when they're walked on, or even worse tip up. In future give the back of the flags a coat of diluted pva 5-1 minimum, this will stop most of the wicking and provide a better bond and buy decent slabs next time :-). Stay safe.

To be honest I think it's a different reason and this might due to manufactureing of the slabs. Try this link. https://www.pavingexpert.com/repair-alteration-and-maintenance-of-paving and look for Circular Marks on Flagstone Pavingots . Lots to explain but this link might help you.