Initially I had the above schematic for a design.Then I removed all those 0 ohm resistors.
That caused a strange problem. I have the below footprints U1, U9. Pad 2, 4 of U1 and the center pad of U9 should be connected to GND. And it was originally as expected. But as soon as I removed all those 0 ohm resistors, all those pads in the footprint started showing connection to +3.3V (attached image below).
I think we need to see the whole schematic. As far as I can see that segment of the schematic should have no impact on power nets. I notice there are a couple of places you have GND net names not attached to anything. Maybe one inadvertently got attached to 3.3V after moving some wires around?