So far, this has happened to me twice. Both times were in Garden of Goo, I had picked up a mineral and dropped the one I was carrying, and the dropped mineral was invisible.
Both times this happened, I dropped the Large size. (Using the Mineral article on the wiki for size names.)
First time it was a red mineral, this time it was yellow.
Made a thread about this myself. Didn't get any attention.
http://forums.spiralknights.com/en/node/7652