There are options with the KM preferences which may help. You can get to them by pressing F2 and going the section named "Content filters" within Page Display. These are not perfect because there are so many ways to produce popups.
We may be able to supply more detailed help if you could tell us the KM version that you are using and supply the URL for a page which causes your problem.
This site
http://popuptest.com/ can help test blocking.
Hanlon’s razor is an eponymous adage named after Robert J. Hanlon that states: “Never attribute to malice that which is adequately explained by stupidity.â€
JamesD