Because of learning and/or evolution. The paper doesn't offer any reason why they shouldn't adapt, as adaptation goes this one should be pretty easy as it is basically just a mindset, probably perfectly doable within the boundaries of learning. So if they become widespread, they will stop being effective, most likely within a few years. Just like the cartoon scarecrow with a bunch of crows resting on it, it wasn't dangerous, so the crows stopped caring.
So, considering adaptation would take years and depending on widespread adoption, this seems a very useful tool to employ for some time. Very far from “stupid things humans do”.
Arbitrarily prefer on bird over another, and believe that you can do something about it with passive-aggressive architecture. That is neither dog stupidity, zebra stupidity nor jellyfish stupidity. That is human stupidity in action.