When destroying a captured UFO in the UFO yard, a confirmation window pops up asking the player if they are sure they want to destroy the UFO. Selecting 'Destroy' here doesn't cause said confirmation window to go away; it merely sends it to the back while the player is shown the updated UFO yard window. Once that is closed, it is still there. When clicking the window a second time, it closes, without destroying any additional UFOs.
Attached is a safefile with UFOs in storage at a UFO yard.