Absence getting auto approved

Summary:

Hi all,

I have come across a scenario.

Time entries are coming from the biometric system with Approved status.

At times few entries with "Submitted" Status

however, what happens is the following:

• Timecard shows as approved.
• Employee raises Late permission(Absence) which goes to the manager to approve.
• Then the process runs Mass Submit and Approve of the day. 
• The permission is being approved without manager approval.

Though we have enabled Absence Approval Routing in Time Consumer Set, despite the absences are being approved, upon running the scheduled process.

Timecard Approval "Auto Approve"

Could someone suggest a work around to prevent the permission( Absences)from being approved if this process runs multiple times a day.