If they installed a keyboard with the same app id (e.g. com.google.[...]) F-Droid would try to update it and ask the user to confirm the update since F-Droid can't update an app that was installed by another app store.
I'd be curious which keyboard this is. Maybe Gboard took over the app id of the previously foss android keyboard.
PS: I recommend F-Droid Basic which supports silent background updates on any Android 12 without root.
The app it wanted to install was its AOSP, it's likely that I was using another AOSP build at the time but I'm not sure. I've used either AOSP or gboard almost all of the time, so it's 99% likely to have been one of those two.
The AOSP keyboard was available on f-droid when I installed f-droid, and the f-droid app kept nagging me to replace the keyboard app on my phone with the debloated AOSP version from f-droid. Debloated, in this case, meaning without support for minority languages such as mine.
There's nothing intentional there. If the keyboard you had installed was also distributed via F-Droid using the same APK identifier, then F-Droid just detects an update since it's the same app.
To prevent this (it can happen with most apps distributed both on the play store and F-Droid) you can tell F-Droid to ignore updates for a specific app.
