The points don't get subtracted as soon as you place something, and especially in cases where costs are meant to go up (i.e. placing an additional coriolis or tier 3 station) you can get away with placing another construction that you shouldn't be able to afford... and when the points correct themselves, you end up with negative values.
It's yet another case of validation only being done in the client rather than on the server end; the game client hasn't been informed that you've spent the points (or that the construction costs have gone up) so it lets you spend them again.
but I watched every one of my constructions, paying attention to the points as I went along, watching it and it be wrong, after the tick it would usually adjust itself back to what I had calculated, I watch it not move after I construct something and have to wait sometimes until the construction site leaves. I had 5 T2 points, I had 8 T3 points, I was constructing a T3 Ocelis that had been queued up before the tick. I have 7 refineries, high tech Odessey ground= 2 T3 points, space hospital, 2 high tech space research, 2 Odessey extraction= 4 T3 points, government building, horizons high tech ground instillation, space security, Coriolis as primary. 3 satellites, 4 comms, 5 relays, T1 ground security, 2 security outposts, 2 space extraction, 5 space farms, T1 ground extraction. T3 ground port is built. So that is 20 T3 points -12 for the ground port and Ocelis space port, so 8 is the right number, then the Coriolis was queued and I had 0 T2 and 8 T3 points. Once the Coriolis was built it didn't change, I waited, and went and docked, looked at the market, and then looked at the system map to see 2 T2 points and 3 T3, so I looked again at what it would cost to build Orbis and it was 18. I am not sure what to do, I don't want to construct more until it is fixed, I will not have enough slots for 18 T3 points even with the extra T2s.