Typically, pop ups are considered to be annoying, with many browsers disabling pop ups by default. Sometimes they go behind the main browser window and creates additional usability problems. So its not just advertising that brings down the pop up's reputation.
In your case, your users already trust your application as they're presumably uploading some data to your server. I'd also assume that the errors you're talking about would need to be referenced by your users in order to fix problems with their uploads.
For your particular case, you could consider the now widely used overlays.
Overlays are now being used on most popular websites, extensively for providing user help. You can read more about this here. The primary advantage of an overlay is that it would allow the user to interact with your primary browser page while the overlay is open.
Additionally, you can give the user an option to convert the overlay into a pop up box if they wish.
I'd also consider the possiblity of just displaying the errors in a persistent box on the top of the page and pushing rest of the content down.