Yes, Pay At Pump transactions count toward any Transaction Controls set on the card used.

In rare cases a value or volume Transaction Control may be breached by a very small amount, if the current transaction is very close to the breach limit and extra fuel is dispensed due to an air bubble in the fuel line or a minor pump leak. If this extra fuel is the cause of the breach and the Transaction Control is set to Decline, in this scenario the Transaction is unable to be declined however it will be included in the breach report.