This is quite the mission bug.
Playing my lowly advent as the upper-lvl soldier game is boring beyond belief...
Anyway, picked a lvl 40 mission (first mission in a couple days with this toon) in Rome Green with the pickup and describe item being a nano crystal and the reward a Blue Man Group Chilled Plasteel Armor Helmet.
Go through clearing the mission, no X% chance of mission token message coming up (a posted change somewhere?) which I thought odd but also thought yeah, maybe FC did change it.
Found the item - it was a ql 39 Cast-Off Plasmaprojector. Mission obviously didn't end, no reward and no token.
Game-play bug to say the least...