Your Level Editor is most likely not placed in the correct directory. In order to function correctly, the Level Editor (and all other HPL2 development tools for that matter) MUST be located in:
Windows:
Retail: C:\Program Files\Amnesia - The Dark Descent\redist\ (or Program Files (x86))
Steam: C:\Program Files\Steam\steamapps\common\amnesia the dark descent\
HINT: Should be where the Amnesia.exe and the Launcher.exe is located.
Linux and Mac should install to the appropriate folder.
If you're on Windows and you wish to have the Level Editor located somewhere else, you're best to use a shortcut link to it, which is easily made by right clicking the Level Editor and selecting "Create Shortcut". This can be placed anywhere and will not affect the way the Level Editor is used or works.
I'm unsure if shortcut links exist on Mac or Linux.