Archive Page not Sorting posts

Hello guys I am a new php programmer still studying the wp codex. I got this job keeping this newspaper working and just today as I updated wp to version 3.5 the article categories of the site are not rendering posts separated by categories as it was. I did read troubleshooting 3.5 but did not find anything that could relate to this issue.

You guys would like check it out at http://www.boavistaja.com
its not apparently clear but if you pay attention the posts categories for example “Boa Vista” has posts from all other categories.

Many Thanks guys