@techee I'm opening them by double-clicking the file in finder. I made a screen-recording to show when it happens:
https://www.dropbox.com/s/i3c58o32yrjdmoj/xml_open.mov?dl=0
File -> open, and dragging them into the already open Geany window, don't make it open a new instance. It's just that the double click in finder started behaving like this. I've used Geany for many years and always opened files from finder, this never happened before