This has been bugging me for a while, where Ctrl+< key> combo uses the first keyboard layout in the list.
I finally found this bug report:

Ctrl+<key> sends erroneous value when primary keyboard layout is not English
https://bugzilla.gnome.org/show_bug.cgi?id=589557

the gist of it is :

A workaround for this entire problem is to NOT set up multiple layouts in
GNOME's keyboard preferences dialog. Instead, use the setxkbmap command to
manually switch between your desired keyboard layouts. For example:

setxkbmap dvorak # switch to Dvorak
setxkbmap us # switch to QWERTY
    - comment 9, Suraj Kurapati

https://bugzilla.gnome.org/show_bug.cgi?id=589557#c9

Thanks Suraj Kurapati!

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