Sorry, so you are using "Hole Series" from "Assembly Features" by selecting Existing Hole in the first component?
FIRST: How do you create the hole in main component, using Cut-Extrude OR Hole Wizard?
Second: Existing Hole in Hole series don't work with Cut-Extrude feature, ONLY work with Hole Wizard. Please see my sample.
Use Hole Wizard in Part.
Then Hole Series only will work.