What is the current
when you see this voltage mismatch? If the current
is high then it is likely conductors that are too small, poor connections, or something similar and you are losing power (and heating
wires or connectors).
On the other hand, if the current is low when you see this mismatch then it is unlikely that it is wiring/connections, instead one (or possibly both) of the meters is wrong. If you can stop the current entirely and still keep the MPPT meter display up, if there is a delta
then the problem is in the meters. If there is no delta
V with no current then the problem is in losses between the controller and battery. In that case you can beef up the wires and/or add a sense wire if the controller accepts same.