I’m using Glyphs 3 ver.3.0.1 (3033).
When double clicking on a component (twodotshorizontalbelow-ar inside the yeh glyph) rather than opening the twodotshorizontalbelow-ar glyph in edit mode, the glyph directly below the yeh is opened.
So if I have the below text in the window:
لندي
lskie
my double click on the twodotshorizontalbelow-ar will open an edit window for the lowercase s.
If I delete the lowercase s, and repeat the double click, an edit window will open for lowercase l.
The text setting is RTL when this happens.
Can you send me the file?
Sure.
Test-comp_ref.glyphs (25.1 KB)
Thanks. 
Works fine for me. Does it still happen when you restart Glyphs?
Yes, unfortunately even after a reboot the problem persists.
Do you have a custom GlyphData.xml? And can you start without plugins?
No, I don’t use a custom GlyphData.xml file.
I have deleted all plugins and emptied the temp folder but the problem still persists.
I’ve managed to stop it from happening.
It was being caused by automatic alignment being switched on for the twodotshorizontal-ar inside the yeh.
Does Glyphs 3 handle the references differently to Glyphs 2?
It seems that the auto alignment is being passed to the two dotbelow-ar glyphs (inside twodotshorizontal-ar from the yeh-ar glyph.
Update:
If I start Glyphs with option shift to disable plugins, the dot positioning bug disappears but the double-click bug still occurs.
Any suggestions as to what could be causing this?
If I increase the descender in the info panel to below the dots, the problem is gone.
Now I understand. You have a second line underneath and those glyphs are selected instead the components. You could reduce the amount of text in the edit view or add a “EditView Line Height” parameter to increase the distance to the next line.
Excellent. Thanks for helping me out!