Twice I’ve watched as I received points for a mission completed and then after completing another mission my point total was lower then it was prior to the mission. Case in point the second time this happen, I completed a mission and was at 99,950 only 50 point from my Loki card! I then completed another mission worth roughly 250 points and suddenly my total points was 99,656?! I expect to loose point from being attacked in a PVP event, but on a PVE?
Same here, I’ve completed every mission in Washington once each and I have 105 points total for it. 
Correction.
I’ve now noticed after completing Loki 1 on Hell’s Kitchen that it counted up the 735 points I was suppose to be rewarded. But I didn’t get the Loki card, so looking at the Prodigal Son for points total, I see I didn’t get those points. I then repeated Loki 1 (which didn’t have a timer either) it showed the points being added again, but afterwards still didn’t actually reward me the points!
I can confirm the same issue. All missions have been completed at least once yet I only have around 100 points.
Same here, points are not added 
Hello everyone,
We are aware of the issue and currently looking into it. We will do our best to get this sorted out as quickly as we can.