I've used 1Password for years (Linux+Firefox though, FWIW), and this never happened to me or our family. I did discover though that the autofill basically went by hierarchy in the URI to figure out what to show, so if you specify "example.com" and you're on "login.example.com", you'll see everything matching "*example.com" which actually is to be expected. If you only want to see it on one subdomain, you need to specify it in the record/item.
That it ignored the subdomains fully sounds like it was a bug on your particular platform, because 1Password never did that for me, but I remember being slightly confused by the behavior initially, until I fixed my items.
