My kdf rommy has this problem, one of the slots could not be worn or modified. Submitted two tickets weeks ago, no response from pwe or cryptic so far.
I have encountered this problem before, seems that you must kill all the shards (the mid size ones) before you kill any splinters (the small size ones that came from the shards). If you kill a splinter while there are still shards around, one of the shard will vanish.