Oh, that is a very interesting interaction! A FLYING SCOUT troop, like the EAGLE, can destroy the troops in a castle or outpost, but can not claim ownership of it. The fact the enemy created troops in your army color is quite an interesting bug tho! We will look into that and expect a fix soon. Thanks for the heads up!
That, my friend, is an excellent observation, and you are absolutley right. We recently added coding that allows the AI to use boats, but we haven't yet added the code to have them build docks. We really should just have it that if they can build a dock, they should, since it is basically a goldmine with an added feature. You should see this implemented in the next update)