Can't reproduce anymore, probably the reported bug didn't even occur in the first place. I didn't understand how jigsaw works back then.

"Join type" do not affect structure piece rotation in Jigsaw block. We can set it to "aligned" or "rollable" and the structure piece will still be randomly rotated. If it is not meant to do that, then Mojang should explain, because I didn't find anyone who knows how it works and this is the only logical thing I can think of.

Tested with element of "bastion units"

How to reproduce:
1.Use structure block to generate structure piece that contains jigsaw
2.Copy (Ctrl+MMB) jigsaw with data that will generate structure element
3.Place 2 jigsaws rotated to top with lock on the same side (prefered: east or west)
4.Set "rollable" in first and "aligned" in second jigsaw
5.Try to generate the same elements (may be difficult due to "pool" random mechanic)
6.Elements from both jigsaws can rotate with front in any direction. Not north, not lock direction. 
7.If you can't reproduce, try again. It's just random, so there is a chance that element from aligned will generate with front on north / lock direction