The most common and most likely answer to this crossword clue is the 6 letter word FALTER
I've seen this crossword clue in The Guardian
F
A
L
T
E
R
More clues leading to the result FALTER
Buddy explains!

The straight part
We know that "flag" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case flag = falter.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 FALTER mean?
FALTER noun- Unsteadiness.
- To waver or be unsteady; to weaken or trail off.
- To stammer; to utter with hesitation, or in a weak and trembling manner.
- To fail in distinctness or regularity of exercise; said of the mind or of thought.
- To stumble.
- To lose faith or vigor; to doubt or abandon (a cause).
- To hesitate in purpose or action.
- To cleanse or sift, as barley.