Makemytrip.com - Denied Boarding due to transit visa issues which MakeMyTrip failed to notify Refund issues

On ** Jan **** I booked the Flight from Bangalore to Cotonou onward and return ticket on **th Jan **** and return journey on May *th ****.
As scheduled on **th Jan at **.** pm I was at the Bangalore Airport to Board the Flight I checked in my baggage and was issued boarding passes the KLM flight was operated by Jet Airways. When I was standing in queue at the immigration one of the Jet Airways staff called me and enquired whether I was carrying an Schengen VISA transit through Amsterdam and Paris. I tried to explain them during booking there was no information or notification from MakeMyTrip.com otherwise I could have booked with other airlines. I was denied boarding and made to wait * hrs in the airport till the plane departed to collect my checked in baggage when I asked if the refund of the ticket is possible Jet Airways informed me to check with KLM Flight. Then I contacted KLM Airlines they simply say you need to check with the Travel Agent you booked the flight.
Finally, I took the issue with Make My Trip firstly they told refund is not possible because it is a non-refundable ticket then I requested them that there is no fault of mine and due to their lack of information all this mess happen and they accepted it and was told share the Boarding Pass as evidence. After multiple calls I told the person handling my case is off on holidays and till he returns the case would be pending. Then one more person called me from their office and she was the senior specialist and assured me to initiate the refund. Now out of Rs ***** only mere Rs***** is refund.
I requested them to make a partial cancellation they have cancelled my entire trip without prior consent. Now I have to pay more money for the return journey and now they are blaming Airlines for refund and requesting for partial refund of additional Rs **,*** after much persuasion.