We received an biometric appointment even after our EAD was approved. The LIN number on the new appointment has extra digit than allowed too. Has anybody come across this situation? Either ways we went for the appointment and they redid the biometrics on the older LIN number. Anybody went through similar situation?

That is very unusual. You should also call USCIS and tell them about this, so that they can merge both LIN number to your application number.