I created a part for the Microchip PIC32MX360 here and all the VDD and VSS are power in types. After laying out the board I noticed some oddities and after doing a full audit I noticed that the nets had 3.3V and GND tied directly together even though the schematic has no ties. I put the part in its own schematic and tied all the power to one rail and all the ground to the other. I noticed that if I remove pin D5 that it no longer shorts to the power rail but even after recreating the D5 pin and then connecting it to ground it shorts the entire rail. Any idea from these pictures what I'm doing wrong?
You can see from the pictures the PCB showing the wrong NETs and then from the power schematic picture it looks right and the ground schematic picture also looks right. According to the PCB C2,D4,D5,E5 are one net and everything else is the other net. It appears from the PCB that D5 is tied to E5 and F5 is tied to G5 creating the shorts but the schematic has no defined connections for either of these.