When I try to use autofill on iOS for a site that I have multiple logins for, BT immediately fills the first of the multiple logins. It does not present me with a list from which to pick the login I want to use at that time.
I’m on an iPhone 6 and iOS 12.5.1.
You can add multiple URIs to a single item other than creating multiple items for each site. I think this would solve your issue. If this is not what you want, please leave a reply.