I believe I am also having issues with the beverages not providing the cell rewards when they are completed. I did have a previous issue where I was crashing (hard crash, full PC freeze that required a restart via the power button) during the final cut scene that also could have been a potential cause of the beverages not rewarding the correct cells. 

Attached is a paint image that contains snippets showing that I have completed all quests, completed all beverage runs, and that all cell drops in areas are complete as well, but you can see that I am missing 15 cells in order to unlock the chips for Bunker and Zed.

On a side note, and this technically is another bug, but It is still showing 96% on Life Incubator, Transcendence center, and Hive Mind as it is showing 0/1 for the station keys.