Below save contains a sniper with Stun baton in backpack. If the stun baton is taken into hand, his armor disappears and basic tier 1 armor is shown briefly on the soldier when using the baton:
https://www.dropbox.com/s/pmlmdtp11f60d3f/StunBaton_armor_glitch.sav?v=0mcns
The save also contains a small graphical glitch within the cruiser:
Some areas stay black even if within the same room the soldier should see there (like there sight blocking elements in the way), and my soldiers got shot through the wall of the large room even though the black tile the alien was shooting through could not be passed.