As someone who had never used corporate social media like FB and Twitter (for my own reasons), when I found out about Mastodon back in 2017-18, I decided to join it because of its philosophy and it not being a corporate-owned walled garden. It has its flaws of course. But since I didn't have any preconceptions, I mostly liked Mastodon as it was and didn't find it confusing at all. That's probably because I read up on Mastodon first to decide whether I'd want to try it, so I knew what to expect.
So I can understand how people who had been using Twitter and had their expectations shaped by it would assume that Mastodon was just a Twitter clone, not having learned anything about it beforehand. That's why they were confused and disappointed to find that it was its own thing with its own philosophy, and had existing communities aligned with that philosophy.
Some (not all) of those who saw the differences as flaws, complained that Mastodon was crap for not having certain Twitter features, and some (not all) existing communities didn't take kindly to demands that Mastodon abandon its philosophy and transform itself into a Twitter clone, so there were conflicts as well, and those new people didn't stick around.
OTOH, many other new people found that they liked the different philosophy and those people did stick around, so Mastodon has grown. But IMO since most people like the Twitter-style algorithms and "broadcast/consume" culture (as opposed to Mastodon's more personal interaction culture), Mastodon will always be a much smaller thing. But its existence is an important and good thing, like the quiet room away from the riotous street party, where you can hear each other speak.