Sir Ian McKellen in this interview is telling Graham Norton about Dame Maggie Smith being cross (upset) with McKellen because McKellen has been doing impressions of her, imitating her mannerisms and speech for comedic effect. Thus, when McKellen recounts this to the host Norton, he imitates her voice and attitude by saying sternly,
You've not been doing me again.
to which the cast and audience laugh raucously. What does "You've not been" mean? Well, McKellen is doing an impression of Smith, and Smith is known for her distinctive voice and particular accent. She was born to a Scottish mother and English father, and in some of those dialects, the negation of "you have been" is "you've not been".
In general American English, negative sentences usually contract the auxiliary verb to the negative particle 'not', so they would say "You haven't been", but some UK English dialects (like Smith's) instead contract the subject pronoun to the auxiliary verb even in the negative, as in "I've not a clue how" or "what you'll not do is disobey me".
"doing me again", on the other hand, is referring to doing an impression of someone, as in "I do a great Elvis Presley every Halloween in the karaoke bar". Another dialect thing is that Smith's intonation seems to be imperative rather than interrogative. General American English doesn't phrase questions this way very often, but a good analogue is "I know you haven't been in the cookie jar again", which is clearly a question that the asker expects an answer to. In this example, "You've not been doing me again." is Smith's expectation, and she presents it in a questioning manner so that McKellen has to correct her. This is a common way of expressing disappointment with someone, and McKellen phrases it this way to allude to Smith's many famed stern posh roles as a actress in media such as the Downton Abbey or Harry Potter series.
So in full, McKellen is parodying Smith by pretending to be her sternly chastising him for doing an impression of her. The irony of this is not lost on Norton, and of course Norton points out that
Now you have done her again!
, which McKellen appears to realize, causing him to laugh more.