You tell us? You’ve just levelled an accusation and provided no information about what specifically happened.

In general, a website cannot directly modify or change a browser’s certificate store through normal web browsing. This would be a serious security vulnerability if it were possible.

I've seen the popups too on Firefox Nightly on Android. It seems to be a firefox issue since I have seen this on other sites too

That is probably due to network conditions between you and the server hosting the site, and possibly DNS issues causing your connection to be downgraded or degraded. Perhaps your browser is out of date. There are a lot of reasons that could be happening that have little to nothing to do with the site, which works for me without any cert errors, though I did get a Cloudflare turnstile.