1. Take item out of crate (or just skip this)
2. Use it (or just skip this)
3. Try to put item inside crate from inventory - not successful
4. Try to put item in your hands and than in crate - not successful
5. Try to log out and log in and try steps before - not successful
6. Try to put crate in your hand and put item inside - not successful (only once successful)
7. Roll down and cry that such major bug is out there still not fixed - successful (everytime)

Happens all the time. Something keeps preventing putting items in certain slots of inventory like crates, treasure box, etc. Sometimes you cant take item out, sometimes you cant put it in some slots, sometimes it wont allow put item inside if crate is on ground but will allow you put item inside if you are holding crate in hands, sometimes it just wont let you put that item inside that crate no matter what. Relog helps only sometimes.