Essentially, this issue arises by, firstly, collecting some Nanosuit Upgrade Kits from certain areas. Then, you unlock any of the Nanosuit Modules (in my case, I chose to unlock the 'Extended Cloak' module). You'd equip it and then continue playing. At some point during gameplay (people say during Cutscenes), the said Module you unlocked becomes re-locked and you CAN NOT go back and re-collect the Nanosuit Upgrade Kits.
This specifically occurred for me when I was playing the beginning of Red Star Rising. After I collected the second Nanosuit Upgrade Kit (This one: http://oyster.ignimgs.com/mediawiki/apis.ign.com/crysis-3/3/38/Mission5_17.bmp), I opened up my Nanosuit Module Menu and saw that Extended Cloak was re-locked.
If it helps, I'm playing on a PS3 system. However, from what I've heard, this issue is present on all consoles.
This is a prior thread created on the issue: http://www.gamesas.com/forums/viewtopic.php?p=607733#p607733