It sounds to me like something is causing your Pipeline Phase field to be updated multiple times in quick succession. Even if the value of the field is not modified, a workflow or some other action can still trigger the field to read as changed.
Open https://make.powerapps.com and go to your environment and then the Opportunity table. Find the Pipeline Phase field, and click on "Check Dependencies". This should show you any workflows or business rules that are touching that field (plugins or cloud flows are harder to find). In addition, you can check the Audit history of the Opportunity and see if anything is modifying that field in separate save actions.
Finally, if you can't determine why the process is triggering twice, you could add a condition to your workflow creating the new record. Simply do a check to see if the [Previous Stage] and [New Stage] are the same. If they are, cancel the workflow without creating a new row.
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