What you note is expected to happen so there's no known issue. The actions will be completed as specified in the version of the PB that was active when the flow interview record was created.
In other words, the two separate versions don't affect each other.
- Version 1 was active, the record met criteria, and a scheduled action
- Version 2 was activated, the record met criteria, and a scheduled
action was queued.
- Version 1, now deactivated, will not re-evaluate the entry
criteria and will not affect the behavior of Version 2. The only thing that
will change is the timing of the action if the date field it relies
on changes per documentation.
After you deactivate a process, the scheduled time for pending
scheduled actions stays the same. If a deactivated process has pending
scheduled actions and the record whose field the schedule is based on
is changed, Salesforce recalculates the schedule for those actions.
After a process is deactivated, Salesforce ignores all other changes
to the associated records."
There's the following idea asking that scheduled actions play nice when activated and there's several questions/resources about this behavior with all the pains it comes with:
In terms of workarounds, there's no "easy" one if you're already in this position.
Your "best" option is to mass delete existing flow interviews for that deactivated version to allow your new version to be the barrier for entry. If you did need some existing queued actions to fire, you would then need to data load the records based on your own manual SOQL/analysis and essentially re-trigger them.
Otherwise, it's best to come at this from a design point of view to avoid it completely.
- Use scheduled paths in record-triggered Flows. See this question to confirm they're not afflicted with the same versioning issue. You should be favoring Flow over Process Builder at this point for any new automation.