The most common and most likely answer to this crossword clue is the 4 letter word CORN
I've seen this crossword clue in The Guardian
C
O
R
N
More clues leading to the result CORN
- Cereal company supported by sailors
- Wow! New for old material
- Ignore economic regulations primarily to monopolise wheat
- Trouble afoot, with commander oppressing sailors
- Yellow food, cheesy stuff
- Either end of a carton of cereal?
- Study involving the origin of rye and another crop
- It’s old-fashioned grain
- Gosh, Beethoven’s Ninth is old-fashioned stuff
- Something old-fashioned in review of ‘Brighton Rock’
Buddy explains!

The straight part
We know that "Trouble afoot" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case trouble afoot = corn.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 CORN mean?
CORN noun- The main cereal plant grown for its grain in a given region, such as oats in parts of Scotland and Ireland, and wheat or barley in England and Wales.
- Maize, a grain crop of the species Zea mays.
- A grain or seed, especially of a cereal crop.
- A small, hard particle.
- To granulate; to form a substance into grains
- To preserve using coarse salt, e.g. corned beef
- To provide with corn (typically maize; or, in Scotland, oats) for feed
- To render intoxicated
- A type of callus, usually on the feet or hands.
- Something (e.g. acting, humour, music, or writing) which is deemed old-fashioned or intended to induce emotion.
- A type of granular snow formed by repeated melting and re-freezing, often in mountain spring conditions.