1. Open a Nautilus window to the target directory you want
2. Plug a USB key or SD card, a new window (rightfully) opens.
  (otherwise just open a new window yourself, doesn't need to be a USB key)
3. Move some data from one window to another
4. Once the transfer is finished, click somewhere in one of the windows.

Result: the popover is dismissed from one of the windows only, resulting in the other window having a status indicator menubutton showing up at 100% permanently until you realize you have other windows (sometimes in the background) blocking the popover open. This rapidly becomes hell if you have 3-4-5 windows like I often do.