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.
Any assistance would be appreciated.