So I selected the native segwit account to send BTC. When it went through It ended up in the Legacy account and not the Native Segwit Acccount. What the heck?
Is this going to be a problem?
Well.... It's not going to be a problem if the address that was finally funded was generated by your ledger... If i'm not mistaking, a ledger allows you to have different "kinds" of wallets next to each other (p2pkh, sw, native sw), so if binance finally funded the "wrong" address, it's probably because you selected the "wrong" wallet to generate a receiving address.
But, as i said, as long as the legacy address that finally received the funds is part of your wallet, nothing really bad happened... You'll just end up paying a couple cents more when you decide to spend those funds.
Do double-check you weren't a victim of a copy/paste virus or a phising website!!!