Sometimes you just have to ignore ERC/DRC. In the end, it's your design and you should understand what works and what doesn't. There are a number of symbols out there that have questionable choices of pin type. Knowing the circuit, I just ignore the error. Also, I have a couple of connectors that the courtyard is just a little too large and gets flagged in DRC when I butt them together. Since I know it's not a problem, I don't bother to go back and update the footprint. It forces me to go and verify spacing.