First of all, thank you for publishing Pico-PIO-USB!
pio_usb_device.c contains a few gpio_*_mask statements that were introduced in commit ef9d780. Specifically:
128: gpio_clr_mask(1<<3);
138: gpio_set_mask(1 << 3);
202: gpio_clr_mask(1<<4);
These statements look like debug statements that were left in the code by accident; In projects that use GPIO 3/4, I think they might cause issues.
Do these lines still serve a purpose?