Difficult to say for sure without the cad file.
But, my guess is that you have 2 bodies. To cut one from the other you need to pad both then use a boolean operation to remove one from the other.
Also, since the second body, when padded, would break the multiple solid rule it will fail at that point.
So, you could extrude the sketch with holes in Part workbench, then cut the extrude from the first body.
Yeah, the multiple body rule gets us all.
Keep askin, we'll keep answerin.