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I could be wrong, but I don't believe the issue is that Alteryx is invoking the same workflow multiple times. My best guess is that your workflow when ran from Gallery is processing a different set of information vs. what you used to develop the workflow with. The "Render" tool will output a separate report for each record it receives. There may be something that you need to adjust in the workflow to account for any differences for when the workflow runs on the server using the default "Run as" (or service account) the server uses.
Your post doesn't give us much to suggest other reasons so if the above is not connecting the dots, please respond with more details to help us understand your workflow design. Sharing screenshots and/or copies (generalized or not) of your workflow will get you the best support from this community.
I, too, have noticed intermittent cases of job duplication. Typically, the second job is created within 15 seconds from the originally created job. I have an active ticket with Alteryx to identify root cause.
Definitely sounds odd. Not saying this is the reason, but based on my understanding on how the controllers design, if the controller fails to receive the status of a job it assigned to a worker, it assumes the worker failed to work that job and the controller will reassign that job to the next available worker. It's possible that something interrupted communication between the worker and controller (less likely if all is on one server, but still possible). Maybe also check to see how system resources are being consumed and not hitting/staying at 100% used for long periods which is typically caused by the server configured to handle too many simultaneous jobs than its resources can handle. This setting is often overlooked and a common issue especially in organizations with an increase of users interacting with your Gallery.
Review the AlteryxService logs as that may include some details to why a job is being restarted.