Nope, it seems to be something deeply in Notepad++, as I managed to reproduce this in freshly downloaded ZIP file.
Here's what I did:
Downloaded freshly, brand-new "npp.6.5.2.bin.zip" file from N++ website and extracted it into "c:\npp.6.5.2.bin" folder.
Opened Notepad++ from "c:\npp.6.5.2.bin" folder and opened any example text file in it.
Spaces in the beginning of lines appeared after changing language (see attachment).
Because font is much smaller than in my configuration, there is fewer number of spaces, but still they can be easily spotted.