Most IP Phones will show multiple "lines" registered to the same extension on their web interfaces even though there's actually only one registration.
So, for example, if you configure a Mitel 6737i to connect to a single FreePBX extension, the phone will show that Line 1, Line 2, Line 3, and Line 4 are all registered to that extension. There's actually only one registration, but this is how the phone shows the user that all four line buttons can be used to make and receive calls from that extension. It's true even if you actually go into the web interface and configure line 1 and line 2 with the same information. The phone knows that what you're trying to do is allow both line buttons to manage the extension. It doesn't actually perform the registration twice.
I suspect that's what you're seeing. There aren't actually three lines registered with the same extension. If there were, I'd expect problems, i.e. inbound calls would show up on line 1 at times, on line 2 at other times, and on line 3 at other times, seemingly randomly.