We used to have similar issue with ghost processes, - when restart was initiated from the control panel, the old process was not terminated (but Centova already expected it to be terminated), then new, restarted proces, was unable to start because of "Port is already used by another process" error.
This only happened on Debian OS (at the same time Centos servers were not affected by the issue). And it resolved by itself I don't know how or why
It was either some update in Centova or in Debian that made it work properly.