I think it’s fair to say that “swapping” the symbolic colors with each other would be an antipattern in most cases.
But here’s one scenario. Let’s assume the app in question is used for therapy or meditation[0] and its primary color is a sage green to emphasize calmness and a connection with nature. (BetterHelp is an example)
In this case, red over navy green is one direction you could go in. But another direction might be a notice with a darker green background and a large white error graphic (bold exclamation marker with a circle or triangle). The header could read “Error” in bold and the error message could appear in white.
To me the dark-green/white mixture would just as clear and usable as the red-over-green method.
Please be unique in other ways.