I do not experience this behavior on stable, using the mouse or super to activate activities. Application windows gain focus when selecting with the mouse, or keyboard using → ← + Enter
I do have a somewhat tweaked environment and don’t use any menu style extensions. For reference my active running extensions and a easy way to list / view then:
$ gsettings get org.gnome.shell enabled-extensions | tr "," "\n" |tr -d "^ ' [ ] " | sort
appindicatorsupport@rgcjonas.gmail.com
cast-to-tv@rafostar.github.com
clipboard-indicator@tudmotu.com
drive-menu@gnome-shell-extensions.gcampax.github.com
gamemode@christian.kellner.me
gnome-shell-duckduckgo-search-provider@keithcirkel.co.uk
gsconnect@andyholmes.github.io
multi-monitors-add-on@spin83
native-window-placement@gnome-shell-extensions.gcampax.github.com
pamac-updates@manjaro.org
pop-shell@system76.com
screenshot-window-sizer@gnome-shell-extensions.gcampax.github.com
sound-output-device-chooser@kgshank.net
syspeek-gs@gs.eros2.info
system-monitor@paradoxxx.zero.gmail.com
systemMonitor@gnome-shell-extensions.gcampax.github.com
topiconsfix@aleskva@devnullmail.com
unblank@sun.wxg@gmail.com
user-theme@gnome-shell-extensions.gcampax.github.com
workspace-indicator@gnome-shell-extensions.gcampax.github.com
To me the issues look like a extension issue that you both experience, comparing the active extensions and some testing might reveal a common source of this behavior.