[help] strange El Capitan bug

Ever since I upgrade from Mavericks to Yosemite there's been this odd thing that before I can click on a ui element I have to click outside of what ever is opened before I can do anything within said window. I mostly see this happen in chrome but have seen it here and there in other apps. It didn't start happening till I moved from Mavericks to Yosemite and now El Capitan. I did run the betas for both and first had the bug appear in the Yosemite betas and has been there ever since. Any help would be appreciated. Would have searched but didn't quite know what to type in the search box.