Interesting. We haven't had the opportunity to use our two battery matrice to its fullest extent yet because we don't have an area big enough...
We currently are using a 25 minute mission timer for the Battery Limited operations because it gives a somewhat reasonable mission plan for battery limited operations and is more than any single battery will last. An unintended side effect of that is that we have not provided a long enough time period for the Matrice with 2 batteries.
Is it turning around to head home at 25 minutes? This would be why.
Our next release will have this limitation removed and will allow all aircraft to fly to the end of their batteries.
There are some other Matrice only concerns. Due to DJI waypoint flights having a limited flying distance of 10 km on all the other aircraft, the extra battery for the Matrice will allow you to easily exceed this. There is new firmware coming out for the other aircraft that is lifting this limit and Map Pilot will support flying longer distances in the next version.