Edit mates to place it on the other face.
Heavy Hex Nuts or Flat Washers sometimes are placed opposite on the axis as I'd like. I take the auto sized part, auto-placed wrong, and accept what has been done automatically, then alter it for desired results. It's not like I had to manually add these mates or specifically select my component.
Take what it is and don't expect it to be a mind-reader. This can happen easier in more complex assemblies. Tiny shifts in mouse movement can alter smart mates placement. Check the results, correct if needed, and proceed.
Yes I get the same problems as you, smart fasteners don't seem to work correctly with more than one plate.
I ended up just dragging and dropping bolts / nuts and washers fro the toolbox in an assembly then patterning.
I did just post something on this but have since deleted it.
Mark (SolidWorks 2018)
Then this "Smart" feature is just a joke ?
Bolts is to fastern minimum 2 plates, I am sure there is a trick somewhere !
There may well be a trick to using this feature but I couldn't figure it out yesterday so like I said ended up just dragging an dropping bolts.
Rather than just selecting one face I though you may have to select the extreme faces on the outer plates so (un)smart fasteners knew it had to go through more than one plate but couldn't get it to work.
I hope some expert can jump in and explain ho you can use this feature through more than one plate, there probably is an easy way to do this.