Thanks for your question.
The two corporations would be considered a controlled group. Yes, only one surtax exemption is allowed. But the $50,000 surtax exemption amount may be divided among the corporations (apportioned) in any desired proportion if all members agree to the apportionment plan. If there is no apportionment plan, then the $50,000 exemption must be divided equally ($25,000 exemption per corp.). This can be elected on Schedule O attached to Form 1120.
For more information, see http://www.taxalmanac.org/index.php/Reg._1.1561-3
Hope this helps,