This because it creates a legal cold war. Some companies just patent stuff so they can sue bigger companies and their competitors for damages. And this stifles innovation because it makes it impossible to compete alongside competitors.
They sue you for your websites one-click shopping cart, then you counter-sue them for the interface they used on their site. They sue you for a javascript for some scrolling text then you patent a unique button design used on their site just so you can sue them back again.
In the cold war this kind of buildup of arms or in this case patents ready for legal engagement, was called MAD (Mutual Assured Destruction) and this is wrong.