For the workspaces published on the FME server, a setting would be good, with which you can choose that this workspace can only be started if it is currently not running.
So a parallel execution can be prevented.
Thus, when using multiple engines can be prevented that the workspace is carried out in parallel and thereby disturb themselves.
Even using just one engine, it may make sense to stop this process from queuing up.
Related:
https://knowledge.safe.com/content/idea/38384/fme-server-gui-option-to-allowdisallow-concurrent.html
https://knowledge.safe.com/content/idea/54199/allow-to-define-maximum-instances-that-can-run-sim.html