Engineer: Damaging / Destroying aircraft with AA Launchers doesn't track.
Recon: Spotting enemies on objectives with gadgets doesn't track.
Support: Airburst incendiary damage doesn't track.
I'm sure there are more but these are the ones I've noticed, and no one has found a work around for.
I've not tried the Engineer challenges yet, and I'm currently suffering through the incendiary Support challenge now (it only tracking direct hits like An4rchy950 mentioned is, unfortunately, fairly well-known now and really needs to be fixed), but I completed the Recon assignment for spots without any tracking issues.
If it helps at all, I did the Recon one by playing Breakthrough, dropping TUGs on the objective (slightly easier as a Defender of course), and then flewing around with the drone.
The airburst one I was having issue with too, you need to direct hit for it to track. Im about 400/500 damage now, get about 25-50 per direct hit on a player with it. Idk if they did that intentionally but its kind of dumb if it was intentional
