We assume that the transmission coefficient is constant outside the transmission window, thus, if this is not a good approximation for your system you must include more energy points.
The conductance looks strange, please try to redo the conductance calculation with 12.2 since we have changed the integration routine, and it should be better now. 12.2 is backwards compatible, thus, you do not need to redo the transmission calculation.
If it still does not look correct please attach your input or nc file ( or send to info@quantumwise.com) so we can check it.