I think the best option is to use a AC adjustment like "Armour Class Bonus" set to the same as your shield that you can turn off when you equip the crossbow.
NOTE: I just went to test this and made a low level fighter with armour, heavy shield and heavy crossbow. After equipping the armour and shield, I equipped the crossbow with one hand - and didn't lose the shield AC bonus. Equipping with both hands only gave me a red warning - "Can't have an off-hand weapon with shield" but I still have the AC bonus.
So, maybe you do have a bug. You can contact Lone Wolf PF support through:  
http://www.wolflair.com/support/report-pathfinder-bug/?project=pathfinder 
Explain what's happened and maybe include a copy of your portfolio with that character. They won't always notice what's in an individual forum post.