Lots of sedimentary stone contains pockets of iron ore some a lot more than others. Two pieces of stone from the same quarry and cut from the same block can vary massively as one can contain a lot and another almost none. Identifying the pieces should firstly be done at the cutting stage and again at the laying stage although it can be difficult to tell as the ore is embedded and some times difficult to detect. I have known a saw man to use magnets to check the stone. Now if the paving has a high concentration the ore will begin to oxidise (rust) and absorb into the stone as the paving will be wet a lot of the time. You can keep cleaning away the rust but it will always return but less each time or until the ore has gone but generally this takes a very long time. Allowing the paving to weather will help the darker patches to not appear so severe. It is a natural product and flaws like this are quite common, liken it to knots in wood.

If you have circular staining on the flags it might of been spot bedded causing moisture to appear where the mortar is in contact with the flag.Flags should always be laid on a solid bed and the underneath coated with a slurry mix preferably nhl lime before bedding

Should have gone to the supplier and asked the question not the contractor

I'd also agree with a previous answer to maybe check the slabs have not been spot bedded, try tapping on the slabs with your nuclear or something hard and it should sound solid and you shouldn't hear and hollow spots that sound like there echoing