Prevent click event on page refresh

You can use Response.Redirect to the same page to prevent the page refresh. Let us suppose you are in the page1.aspx button click event then on the button click event use Response.Redirect("page1.aspx?isPopup=ture"), in the page load you need to consider to load pop popup based on the query string value.

Are you using Asp.net forms?

That should not happen. Are you calling the function from any .Init() function call? Because upon the page refresh, button has no way to be clicked automatically, unless server-side or a client-side scripts does that.