Pinholes in new cast iron pan
Have you seasoned the pan yet?

https://www.southernliving.com/food/how-to/how-t0-season-a-cast-iron-skillet

I think the oil you use for seasoning will fill up those holes.  The other thing about a pan is that it gets hot and it is going to be hot in the holes.  No germs will survive down there.