FWIW, I've been seeing this (and a related problem) for a long time. Specific to the custom autofill settings mentioned above, it hasn't worked the last couple months.
But more specifically, the Android app does not prioritize/rank the multiple logins properly like the Chrome extension does.
If I have separate logins for:
* site1.domain.com
* site2.domain.com
* site3.domain.com
and I visit "site3.domain.com", I'll see the Android autofill suggestions in a random order. Usually "site1." is first. If I do the same on Chrome, then "site3" is the first result (this is as expected).
This has been going on all year.
