I was halfway through season 2.
At this point it won't even retrieve info I already have.
Try choosing just one episode you don't have info for and doing get tv and movie info. Doctor Who is a tricky show to figure out because of the reboot in 2005, and all sorts of different naming conventions. When you choose a single episode look at what the TVDB is using as input and its suggested outputs. Pick one that woks for the episode you selected if you get the choice.
If that worked, pick two further episodes and try the get info thing again. This time it should be automatic, and the info should be consistent with the single episode you picked earlier. If this step works, you should be able to select the whole bunch and try again. Now TVDB and MC will know exactly which series ID to use for your files.