You have a number of problems, but the pcb holes are because the pins are defined as female rather than male (which is usually what they should be.) TerminalIds are missing in schematic so it doesn’t render correctly
the miso pin circled in green has a correct terminalId the wire connecting in the center of the pin (and likely the schematic being 0.05in off the grid) are caused by the lack of a terminalId. The wire will connect in the middle of the pin. Pcb looks to have a scale problem in that I assume the board should fit in 0.1in headers and it does not. It could be 2mm connectors but it looks wrong for that too.
