Sir,
As per abatement notification no. 26/2012-ST, service tax on GTA service shall be calculated in the following manner: (25% x value of service) x 12.36%
This entire amount is to be deposited by the service recipient. So answer to your first query is that the remaining 75% is an abatement which need not to be paid by any party.
Secondly, presuming that you are not an individual assessee, it is wrong on the part of your GTA vendor to charge 25% of 12.36% in the invoice because as per notification 30/2012-ST, 100% of service tax for GTA services shall be payable by the service receiver only. This service tax should be paid by you directly to the department and not to your vendor. Hence, you should ask your vendor to revise his invoice.
However, if you are an individual; assessee, the practice is entirely correct and you can take credit of 25% of service tax amount as a Input Service Tax if the same qualifies as your input service as per CENVAT Credit Rules, 2004
Further, clarification on the above issue can be given on the basis of your nature of business/ transaction.