Such URLs are usually generated for components, that do not have direct JoomSEF support. I would advice you to check what component is producing these (you can identify it by looking into the JoomSEF URL list) and switch the SEO URL generation off (or to no-cache) for this component.
If components generates such URLs, it means, it is written in a way, that does not work with JoomSEF out-of-box and that to have a \"nice\" URLs for it an special extension will be needed. (as we have for VirtueMart, Fireboard forums, SOBI2 or others).