Situation: Whenever I invade another player's island, I set up like 5-6 military camps around the trade buildings to capture them. After waiting a loooong time, when the timer hits 0 and the ownership is meant to be given to me, they instead collapse and disappear. WTF? How do I stop this and get to keep the buildings? It's making taking over islands extreeemely slow since the NPC just builds a new warehouse straight after.
It sounds like the enemies are razing the building in order to keep you from taking it over. I'm not sure if the likelihood of this increases with the difficulty you're playing on, but in case it does, you may want to try lowering the difficulty.
In order to increase the speed of takeover, I wouldn't rely on trade building capture being your only method. Here are a few steps you can take to speed it up.