User on Record When Salesforce Flow or Process Action is Triggered

This is working as designed. 

Process and Flow rules perform actions 'As' the user that caused them to run.  When a Record is edited by a Flow rule field update, the User recorded in the Activity History and Last Modified By Field of the Record is the User who triggered a Flow or a Process as long as they are still an Active User.

In the event of a Process or Flow Rule Time Trigger updating the Record after the triggering User has become inactive, the record will display the Default Workflow User as the User who edited the record.

Example:

'User Bob' edits an Account and saves it. A Flow rule triggers. That Flow updated the Account 'Type' (either as an immediate action or a time-based action).

Expected Result: Field History shows 'Type' was updated by 'User Bob', because that is the user who caused the Process/Flow to run and update 'Type' field.

To Determine Who is the Default Workflow User

Review the field "Default Workflow User" in the Process Automation Settings as noted here:

Classic: Setup | Create | Workflow & Approvals | Process Automation Settings 
Lightning: Gear Icon | Setup | Process Automation | Process Automation Settings


In the event of a Process/Flow Rule Time Trigger updating the Record after the triggering User has become inactive, the record will display the Default Workflow User as the User who edited the record.