The question is incorrect. It should be: "What are you doing in here?"

No. It should say, "what are you doing in here?" Or "What do you do here?" (if they work somewhere).

I have no doubt that what you heard sounded exactly like "What do you doing here?" That's because quite often in everyday speech,(when someone is not careful about pronunciation,) that sentence will be pronounced like ''wha duh you doing here." The ''t" in ''what' will be pronounced as a ''flap,"that is the tongue does not rise slowly to the palate and then come down. Rather, it just flicks the top of the mouth very rapidly. At the same time the vocal cords vibrate, as they do when pronouncing vowels, and the resulting sound is like ''d.'' I think that the sound you heard is the most common way that Americans pronounce "what are you..." You apparently have a good ear for language.

Arthur, Okay. I hear, What /ə/ you doing here? This is the weak British r sound. It is not easy to hear, but it is definitely there. She uses good classical pronunciation. If she were American you would hear, What /ɑː(r)/ you doing here?

The sentence isn't correct. The correct sentence is " What are you doing here?"