You should have been suspending disbelief for every episode and not just the recent ones. It's always been a show about a alien who time travels in a blue police box. Not really scientifically based.
There's a difference between buying into a concept and looking past plot-holes. With any sci-fi or fantasy story, you have to allow the story to bend/break the rules of reality when you accept the concept, but to be successful it has to make complete sense after that.