Are you assigning the inner layers as Plane or as Signal layers? If you assign them as Signal and place your own Copper Areas then the Keep Islands Y/N option should be available as it is for Top and Bottom layers.

Yes that works, but when I add a via it always conflicts with that layer (yellow cross). I can't easily tell if it's just the GND layer or an actual problem with a trace or something.

You probably have to assign the GND Plane layer as Signal and manually place a GND Copper Area instead.

"I can't easily tell if it's just the GND layer or an actual problem with a trace or something." The information in the left hand panel of the PCB Design Manager should tell you when you select the DRC error/warning.

Ok, so I understand there is no option to ignore islands when a layer is set to plane. "The information in the left hand panel of the PCB Design Manager should tell you when you select the DRC error/warning" Maybe I was not clear enough. I'm looking at the yellow cross on my via and move the via until there is no cross. I don't click on DRC or check the design manager every time I move a via ever so slightly. I will continue simply disabling the ground layer until my PCBs are done and check it last. Thank you all for your time.