This happened because Bungie doesn't have its own, "universal" authentication method, but instead uses third parties' authentications like PSN and Live, which can be moved around between accounts. As long as you keep one authentication account connected to your Bungie account, you'll be fine. This is useful because you don't have to deal with making more accounts (all you need is your PSN/Live/b.net account to start playing), but the downsides are as you see here: You can end up with multiple Bungie accounts if you don't link them properly, and accounts can be orphaned if you move authentications around.
So here's what you should do to avoid this.
If you're an old player:
- Log in through PSN/Live.
- Go to your settings > Account & Linking.
- Link your account.
Do NOT:
- Log in through a different account, like your Battle.net's. That makes a new Bungie account.
- Link your authentication account to the new Bungie one. Your other Bungie account will lose its authentication method, and have no way to log back in.
New players do not have to worry, since you'll be making a new account anyway. Still, Bungie should make moving authentications around a more
manual process, like you having to go to your account and unlinking it yourself if you want another account to have it.