For anyone still headscratching about these ghost shortcuts
You all know the Mate (=Caja) shortcuts can be changed by control-center -> keyboard shortcuts
But there is also a second set of shortcuts for the windowmanager (in this case: Marco)
That explains that a keycombo that is defined by both will result in two (different) apps launching at the same time when you press a keyboard shortcut.
These windowmanager-shortcutkeys-settings are not found in control-center.
The Marco shortcuts can be found with dconf-editor
it is split up between two locations
Here they are (I'll take the case, where the [windowkey]+[E] is linked to caja, as example):
Important to know is that if you switch from Marco to Compiz, you will have to use the Compiz-Config-Settings-Manager (CCSM) to change the Compiz shortcuts because Compiz does not store its settings in dconf like Marco does.