Extruded cuts don't generate properly when using an assembly-built part

For a project I need to get two plates connected. One is the base, the other a circle, which is a part built in the assembly because it has sketch relations with other parts. I want to get holes through both parts to connect them later with bolts from the Toolbox. But when adding the holes (or any other extruded cut) the preview shows it only goes through the first plate, even though 'through all' is selected. When selecting 'blind', the preview shows correctly. 'Feature scope' is set to 'All components'. When moving on, the hole is created correctly. But when adding a bolt, there is no preview of the shaft (only an orange arrow) and when created the shaft isn't made, just the head of the bolt remains.