The most common and most likely answer to this crossword clue is the 9 letter word OVERRIDES
I've seen this crossword clue in The Daily Telegraph
O
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More clues leading to the result OVERRIDES
Buddy explains!

The straight part
We know that "Manual controls" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case manual controls = overrides.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 OVERRIDES mean?
OVERRIDES noun- A mechanism, device or procedure used to counteract an automatic control.
- A royalty.
- A device for prioritizing audio signals, such that certain signals receive priority over others.
- A method with the same name and signature as a method in a superclass, which runs instead of that method, when an object of the subclass is involved.
- To ride across or beyond something.
- To ride a horse too hard.
- To counteract the normal operation of something; to countermand with orders of higher priority.
- To define a new behaviour of a method by creating the same method of the superclass with the same name and signature.