There are a ton of ways they can spot PBNs. I think the most common footprint PBN owners leave are:
10 posts on the homepage
1 or more links in each post
Full content posts on the homepage versus excerpts.
No internal linking outside of the navigation menu and maybe a "Recent Posts" type widget.
You tie those four things together, and you probably have a PBN site.
However, the biggest way they are finding PBNs right now, in my opinion, is hosting. They can easily infiltrate some of the larger, popular PBN link providers. Buy into them, get a few of their sites, and from there it is a piece of cake to unravel an entire network. Those kind of networks have a ton of overlap in the OBL profile.
Then they take those sites and investigate the sites they are sharing hosting space with on shared servers. If anything even smells like a PBN, it gets the axe. That's why a lot of people with smaller, "private" PBNs were complaining about getting hit when No Hat Digital and Rank Hero went down. It gave the illusion that Google had some more automated way to track down these sites, but really it was just collateral damage.
That is probably why you saw 1 site de-indexed and not the rest of your network.