The most common and most likely answer to this crossword clue is the 9 letter word TWIDDLING
I've seen this crossword clue in Independent
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Buddy explains!
The straight part
We know that "what you’re doing with your thumbs" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case what you’re doing with your thumbs = twiddling.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does TWIDDLING mean?
TWIDDLING verb- To wiggle, fidget or play with; to move around.
- To flip or switch two adjacent bits (binary digits).
- To be in an equivalence relation with.
- To play with anything; hence, to be busy about trifles.
- The act of one who twiddles.