@tcox8 When using Ground Fill Seeds you don’t connect them with a trace. The ratsnest lines will still appear to show the ground pins and connections even after ground fill. To remove the ratsnest; Click on the top menu View, then third from the bottom uncheck Ratsnest Layer.
Never use auto rout… but if you must, manual connect the main pins first (5v, 3.3v, etc.) and then use auto rout.