You know that you have to walk over the point they died to get them, right? ( Just a confirmation) This game isn't getting patches anymore. And what level are you talking about? Eye of the Storm?
Yup. I suppose I really started to notice it once the aliens had been in the game for a while. It was random anyway...the nanoparticles don't hang around much either, unfortunately. So, either they disappear quickly or they just don't appear to start with...wouldn't know what % of Cylons don't give up their nanoparticles...at a guess, I would say most of them don't, e.g. 60% or more.
That very final section where you have the cloaked Cylons, I assume you don't get nanoparticles for them?
Anyway, I completed the game on Normal, with no upgrades. THAT would be a cool trophy to have for doing that, I think! Got just over 38,000 upgrade points...if I decide to replay on Normal - not that I'm keen to - hopefully those points will still be there...so I can try and get some of those stupid trophies I missed out on.