So, I was in an area of the server testing chairs to see if they worked, so then I went into my TARDIS to make a pickaxe.

However, I found that I had TWO TARDIS's. I hadn't placed another, so I don't get how why there were two of them. Granted, it might've been a companions, but I haven't got any companions and I haven't seen anything about them. So, now I'm afraid I might get banned because of some glitch. I've mined the second one, but that probably won't change ANYTHING, to be honest.

tl;dr went to test sitting, found I had two tardis's

Yeah its a glitch thats been in the mod for a while, I wouldn't worry about it

This is a known bug, its not a second TARDIS its only a duplicate of your exterior. If it happens again, break the duped exterior.

I've been having this for a while now and lost some online bought exteriors due to it..

John is working on the 'TARDIS sync bug' for next update, I believe that might be this. If you've lost any stuff you bought online (especially due to bugs), you can get them back. 

 Nice! :D