Footprint pad changes based on schematic

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).

Can anyone please help?

That is very unusual and shouldn’t happen.

Make sure to recreate the netlist in eeschema and re-read the netlist in pcbnew.

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?

Is your EESchema ERC report clean?

thanks. I corrected the GND net names that Nathan mentioned and it looks good now.