Because the top general was butthurt because incompetence in the military was called out. And he didn't want to change things to improve it.
Zelenskyy thought they were causing too much trouble, and chose to fire the by far most qualified, over a run of the mill traditional soviet era general.
No single person in Ukraine has done so much to turn the tide in the war against Russia. Fedorov is a genius, and is the brains behind shutting off Starlink to the Russians. And the extremely successful drone strategies Ukraine have been using for the past 6 moths.

Here is a list of 22 accomplishments he has achieved as minister of defense:
https://mod.gov.ua/en/news/mykhailo-fedorov-highlights-22-key-achievements-of-the-ministry-of-defence-of-ukraine-during-his-tenure

Per this BBC article:

Initial rumours that the end of Fedorov's tenure was related to tensions between him and Commander-in-Chief Oleksandr Syrskyi were all but confirmed by Fedorov himself and Zelensky.

On Thursday, Fedorov revealed he had suggested to Zelensky that Syrskyi and Chief of the General Staff Andrii Hnatov should be replaced.

Zelensky, speaking at a press conference with UK Prime Minister Keir Starmer, acknowledged that the conflict between the General Staff and the defence ministry had been "systemic" and occurred "at various levels", and that Syrskyi and Fedorov would only work together with his mediation.