Not all pop-ups are ads or even all bad. AdBlock Community Manager Rhana Cassidy explains the various types of pop-ups and how to block the ones you don't want to see (and allow the ones you do).
Block pop-ups with AdBlock
I'm going to have to break down the answer to this question into two pieces: first how pop-ups are likely occurring and second armed with that knowledge what you could do.
There's not really a question here. It's just an announcement of some hopefully helpful information I posted on AdBlock's Blog. :)
If you have a question, though, I'm happy to try to answer it for you!
AdBlock Community Manager
There are three ways to stop pop-ups in their tracks: your browser itself, dedicated pop-up blockers, and ad blockers such as AdBlock.