Seems like she didnt tow the party line on justifying the Iran war. She testified to congress last year that Iran did not have and wasnt developing nuclear weapon capabilities, according to available intelligence. She's apparently been excluded from the war room when the Trump regime was planning the attack on Venezuela and the initial strike on Iran, indicating a lack of trust in her that's lasted 6+ months.
My speculation: she was dancing the line between keeping in line with Trump to keep her job, and not trying to be tried as a war criminal after this regime falls. No part of me believes she has an ounce of integrity or compassion, but I can absolutely see self-preservation being more important to her than stroking Trump's ego.