Today on Fedora 40, I hit the error in the title.

The whole error was:

VirtualBox can’t operate in VMX root mode.
Please disable the KVM kernel extension, recompile your kernel and reboot.
(VERR_VMX_IN_VMX_ROOT_MODE).

Solution was easy, I had to remove kvm kernel modules:

sudo rmmod kvm_intel
sudo rmmod kvm