By order ques, I mean if I click somewhere far away and keep clicking end turn the units will continue to head toward that spot.

I did this with my sov's army. I click attack on a city and she stopped adjacent to it with here movement spent.

Since she was adjecent I figured, what the hell, I'll seige the city.

The city then had the seige icon over it. I clicked end turn. My sov then attacked the city under siege and won. Now I owned the city and it was still under siege. Any time I tried to do anything with my sov it said "can't move while seiging". The button was greyed out to enable/disable a siege on my sov. I had to reload to fix it.

Suggested fix. Enabling seige should wipe out the order que. You should also check and see if order ques ignore the digging-in commands as well. Else we could dig in and attack cities with our bonus stats.