Mapped domain indexed twice: as website and as subfolder

Hi,

I have a multisite install with subfolders. Let’s say the main install is in https://www.mynetwork.com and subsites are:
1) https://www.mynetwork.com/subsite1 mapped to https://www.subsite1.com
2) https://www.mynetwork.com/subsite2 mapped to https://www.subsite2.com
etc.

I’ve checked that in google (site:www.mynetwork.com) both versions are indexed: that is https://www.mynetwork.com/subsite1 and https://www.subsite1.com

Time ago I used to add a line in robots.txt like the ones:
disallow /subsite1/

But now I’ve deleted all this “disallow” lines related to subsites, and the subsites started being indexed as subfolders.

Why? How is Google “finding” the unmapped versions? Some of them are mapped years ago, none of them are recent mapped websites.

How can I avoid it?

Thanks