I noticed a bug when we play the campaign. Each time I close the game and go back to my game, it doesn't save all the nanopoints that I have collected. It always reset to 0. If I die and restart to a checkpoint its fine its still here, its only when I close the game because I'm done playing at the moment and open it back. I just wanted to report that bug so it can be fixed in a future patch, but I know that right now they must be busy fixing the multiplayer issues.

im having this problem to, i lose all my nanopoints very often. But i don't think it is just when i quit campaign, because i just killed a pinger, and it said 2000 nanopoints collected, so i go and check how many i got and i only had 200. It would be nice for this to get fixed considering im never going to be able to unlock anything except the cheap upgrades.
oh yeah and when i do end up losing my nanopoints, when i try collecting like 100 from the regular enemy guys, it just stays at zero usually until ive played for a while then it goes back to keeping track.

Yeah I noticed the issue with the nano catalyst/suit upgrades. It is not tied to your save file, but universally somewhere. If you check your NC amount and then load a different save you should still have the same amount, along with your upgrades. I noticed the bug when playing and my game crashed. I was just about to unlock the deflection upgrade and had like 10,000 NC stored up. When I finished a tough fight I was sure I had the necessary NC to upgrade and noticed I only had like 4,000.

So I decided to do some testing. Every time you close the game and relaunch it you lose like half or all of your nano catalyst. This is obviously a huge issue if you play in small increments and if you crash. But if you lost a whole bunch of nano catalyst and want to get it back quickly I found a temporary solution. You can go back to a mission where you fight a bunch of Ceph and collect nano catalyst over and over. As far as I could tell you need to get to a checkpoint for it to save. What I did was go the end of a mission where you fight a Pinger (2000 NC) for the first time and repeat that section over and over.

I did have the same issue where I collected some nano catalyst and it didn't add it or did it in small increments. My guess is the value went into the negatives and it took several collections to get it back to a positive state that the game actually displays. I'm not sure whey Crytek decided to make the NC/upgrades apply universally to the campaign instead of in each save file. Although it is interesting to start the campaign over with all the upgrades. Hopefully they will be able to address this and the other bugs quickly.