Patterns can be touchy. I needed to use eight bolts and washers to attach a port cover, and I needed this in six equal places around a barrel. After much grinding of teeth, and possibly less hair, I have had my way with it. I can't say that all of the steps are vitally important, but this is the way I finally got it to work.
1. Place one cover on a port: The ports are a patterned feature on the barrel, so I made sure to choose the one that was modeled first. Use a "mate" as the first constraint. Next do an insert on the od of the plate, followed by an insert of the first bolt hole in the port with the first bolt hole in the cover.
2. Place a washer: Mate first, then insert into the first bolt hole of the cover.
3. Place a bolt: Mate to the washer first, then insert into the hole of the cover.
4. Group the bolt and washer.
5. Select the washer, and create a pattern by axis; resist the impulse to accept the pattern by reference. Use the axis of the cover.
6. Do the bolt the same way: Select the bolt, and create a pattern by axis; resist the impulse to accept the pattern by reference. Use the axis of the cover.
7. Now that the fasteners look good, group the cover and the fasteners together. In my pictures, you might notice there's a seal in there too, but it doesn't need special treatment.
8. Pattern the new group; pattern by reference is fine here. And there you go, it works!