Doctor Who is an absolute monster of a show. This is a franchise that's been around for longer than Star Wars, and when you look at how long it's been on the air, it's no surprise that things don't add up from time to time.
Contradictions, retcons, plot holes, and out-of-character behaviour are common sights in the show, mainly because the writers can't possibly know every small detail out of hundreds and hundreds of episodes, and also, simply because sci-fi concepts like the ones seen in Doctor Who can get confusing really easily. With a show this big and complex, inconsistencies are simply inevitable.
To explain away some of these niggles, fans tend to use phrases like "timey-wimey" "wibbly-wobbly" and "showrunner bad", but - putting complicated time travel issues to one side - there are lots of things that can't just be waved away, some moments that don't seem to make sense even from a basic logic standpoint. Or at least, the logic that the show presents us.
Whether it's a character appearing out of thin air, or a clear rule that the writers set up, reinforce, and then break, the revived series has more holes than a cheese grater if you want to get really nitpicky. So let's get really nitpicky...