I've been able to find a reliable reproduction. Investigating the cause today
edit: I've confirmed it is something we did in FAF - I'm unable to reproduce it in the Steam version of the game.
edit: I've confirmed that with or without the drag build feature, the queue can become unresponsive for at least one click after a few seconds.
edit: found one case and managed to fix it. You can the explanation on Github #5761.
edit: the drag queue feature appears to be more stable now too. It appears that it won't work if you try to decrease a unit right after dragging the queue.
The fix is now live on the FAF Develop game type. It took about three hours to investigate and fix. With thanks to @silentNoob for his extensive description and video. @silentNoob could you see if you can still encounter the bug on FAF Develop?