Yes, we've seen this a lot as well on WFA 4.1 (have not yet tested 4.2).
The only case where I know this happening for sure is when I change the parameters of a finder that is already in use by a workflow. That workflow is guaranteed to go "zombie" on me.
I've managed to bring a workflow back in the past by editing the backend database using the root login, but it's messy and not at all straight forward. The only other solution I know of is to restore from a backup, fortunately WFA does daily backups by default. Considering how often I've been running in the problem I usually take a manual backup now whenever I start working on existing workflows.