Alert warning. Wary; be cautious. A word or action that makes one suspicious of someone. ‘Flag’ is often used in the sense of ‘to flag someone’ who isn’t working out, so if someone’s incompetence is apparent it ‘raises the flag’ to notice them. (Compare to Trigger warning or Heads-up.)

“When she said she had 10 years’ experience, that raised a lot of eyebrows in our office because she obviously didn’t know her work.”