@peter I'm guessing it's because Mastodon tries to handle web+mastodon links: https://github.com/tootsuite/mastodon/blob/79b34a0fa2e993967f22892b857dcf601c07bd88/app/javascript/mastodon/containers/mastodon.js#L39-L42
In Firefox it also gives a fairly annoying prompt to handle this protocol. But if you click "accept" then it's actually kind of nice, because you can click an embedded toot (e.g. on another site) and have it launch your instance. Looks like Brave isn't surfacing the actual protocol to the user, so yeah I think it's probably bad UX.