How to prevent alerts or confirms to remain open?

In my script, I have some alerts and confirms (e.g. if I detect a problem, I may use a confirm to ask the user if they want to proceed). Now, often this works well, but sometimes the confirm dialogs remains open after I click "yes" or "no". I suppose this is similar to my other problem. I tried to place a app.refresh() after some of those dialogs, but the issue still happens.

Do you know how to definitively solve this issue?