I am having the same problem in campaign but it start as soon as i have to retake the island "treasure" i have also found that any of the tuturial islands also reset the unit load out the that type of mission if you have to retake the islands at any point.
I am able to set waypoints for mantas and walruses with no problem. I now can only move the carrier in direct control mode. The map screen will allow me to Time Warp to other islands. I am very far into the campaign. I have not tested earlier save games, or strategy mode. I'm not sure if this is a bug or an undocumented feature. It does make navigation around islands very difficult, which is required by some missions, where telemetry may be limited.
I can no longer set waypoints for the carrier in Map screen, in campaign
in CARRIER COMMAND: GAEA MISSION - TROUBLESHOOTING
Posted
I am having the same problem in campaign but it start as soon as i have to retake the island "treasure" i have also found that any of the tuturial islands also reset the unit load out the that type of mission if you have to retake the islands at any point.