This is on version 0.61.0 but I've definitely noticed this before in previous versions.
While editing files I can see that there are errors, but then if I run
pkill flow
npx flow # or npx flow check
To approximate how it would run in CI, it says there are no errors. If I make some whitespace changes to a file and save then the errors show up again. This makes running flow in CI unreliable since it passes when there are errors.
Even after running just flow shows there are errors, running flow check shows Found 0 errors.
This seems related to #1520 but that was closed without a resolution.