Tried that several times, from basically every angle. I even tried to use the hook to pull it away from its spot. Wouldn't so much as budge. It's just locked into place.
Viewing post in Voices of the Void 0.8.2 Bug Reports
When you put an item in the blue crates they become "glued" to the crates. If something knocks them out quickly or you pick them up out of the crates it can cause glitches like this. The only way i've found to fix it is by using the crate to scoop it up like the other comment said. One way to prevent this in the future is to pour the crates contents out instead of picking things up out of them.