Copied from a discord report:

I've completed the quests for Sweeper and just now Shroom but their respective chip slots do not activate in the chip menu. I still got access to the skin rewards and the cells that came with the quest. This occurred while I was playing solo. I forgot what team was ran with Sweeper as it happened days ago but for Shroom there was Blaze and Bunker and went Headquarters -> Procedural -> Life Incubator.