As per Dev-A team, the reason netscaler is setting the MSS is because in an intermediate communication the server responds with an MSS of 8960 which is Jumbo frame. However we are not sure, if it’s actually set by the server or some intermediate device, however as a workaround we can set the MSS value to 1460 in global settings but this needs to done during downtime.
In the meantime I am also involving development to look into why netscaler is sending an MSS of 8960 when there is configuration as such. Will keep you updated on the progress of the case.