So I have set my tardis perms to companions and added someone and checked they're in companions and they can't use the door or controls.

Check you've done the correct commands

/tardis-perms companions   (you actually type companions not their username)

/tardis-companions add Username

It doesn't work for me either and i did the correct commands and it said they were added

Are you trying to add multiple people? If so then you need to do /tardis-perms companions each time after you add a new player.