from fact-check.org
Technically, however Obama removed ALL of Bush's ambassador appointees. He left those that Bush had left from the Clinton administration. However all Bush appointees were dismissed. Trump, on the other hand allowed Yovanovitch to remain at her post for 3 years. (She had been appointed by Obama in 2016 and hardly qualified as a "career appointee". Further, reports indicate that she and Trump had a difficult relationship. Allegedly, she refused to display a photo of the president in her offices at the embassy, if true, clearly a protocol breach. Reports also suggest that she was resistant to obstructive in carrying out the requests and demands of the administration.
This is not a good recipe for success when you serve at the leisure of the president. He had every right to remove her at any time, for any reason. There's no smoke here.