One possibility would be for those upstream receptacles to be in plastic boxes with no bond made from the yoke to the ground wire, but the ground wire being properly spliced at each box. This could happen by accident or negligence. (loosening or never accomplished)

They're definitely in metal boxes, I opened all of them up. I was putting a gfci on the first one so I could legally install three prong outlets on the rest. The first 2 show open ground with a cheap outlet tester but the other three on the circuit show equipment ground is present. It's not a bootleg either ground as far as I can tell. I was under the impression that current code required the ground conductor to be part of the same romex cable as the other 2 conductors, can outlets be grounded individually and be in compliance with code? maybe a previous version of the NEC that would be grandfathered? Or is it likely the work of the same fool that wired all the reverse polarity outlets I found and created his own electrical box by chiseling out a hole in a 3 stud corner post?

I assume you are working with 2 wire cable. If the devices are in metal boxes and are wired with bx cable it can fool a tester into thinking it is "properly" grounded. It is simply reading through the ground prong, device yoke and jacket of the bx cable which is NOT approved as an equipment ground.

Nope, it's NM cable. Old 2 conductor with black cloth jacket. There's a bare copper wire in the boxes that test ok for ground, but it's not part of the cable and it doesn't go back to the electrical panel as far as I can tell. I have no idea what it's grounded to. I also have no idea why someone would go through the trouble of grounding all but the first 2 outlets and not just run new 3 conductor cable to everything, it's the same amount of work. Everything is gfci protected now at least. I was just wondering if the ground was a code violation because of NEC 300.3(B) which says "All conductors of the same circuit, including grounding and bonding conductors shall be contained in the same raceway, cable, or trench." But 250.13 seems to say that it's ok to ground replacements for non grounding receptacles seperately.

NEC 300.3(B) has not always been in the code. So installations prior to that inclusion will not necessarily comply. But each code revision does not require that residences be immediately upgraded to the latest code.
There are good technical reasons for 300.3(B).
Those who make up the rules that then become laws do not always accommodate the practical considerations. A separate equipment grounding conductor is not quite as good, technically speaking, as one in the same cable or raceway. But speaking from a practical perspective, it is far better than none at all.
So your choices boil down to using it with the present ground or replacing the complete cabling system. The benefits of the new will be small assuming that all works well at present.
Fishing in a single grounding conductor to an existing box is usually MUCH easier than replacing the existing cable.

Sometime in the fifties it was common practice to run a bare copper grounding conductor to all the metal boxes in a kitchen, and sometimes a bathroom, and ground it to a metal water pipe. This practice is no longer acceptable as once you replace a section of metal pipe with non metallic pipe the grounding path is lost, and if a ground fault occurs you will end up with a section of pipe that is energized.