Browser Prompt Requires An Additional Click Before Other Buttons Are Responsive.

I have a pretty simple argument that I'm trying to implement, but for some reason, the way I have it now requires the player to click an additional time before the game is responsive again.

So an example, player single clicks on the reset button. The browser pops the window explaining that clicking reset again will erase all local storage. If a player clicks on any other button (or really anywhere inside of the game), the game does not register that input. If the player then clicks a second time (let's say on the reset button again) then the action will take place. Is this a functionality of using a browser pop up to display something to the player, or is something running a second time in the background that I am unaware of?

I think when using the browser alert the ok button of the alert gets focus (so the game window isn't focused anymore)

Ah okay. That makes sense and I kind of thought it was something like that. So I guess the only way to avoid that is to make a "pop up window" that is built into the game itself?