Please link us to the page with the issue so we can check it out.
What usually causes these problems is the addition of content that is wider than the column it is in. Did you add a photograph or video recently? Or not put a link into its property HTML form (so it looks like a long bit of code rather than a linked word)? These will all push the content containers around which can push your sidebar over or down.
Did you try switching Themes to see if it happens in another Theme?
run the validator http://validator.w3.org/ and check for unclosed or extra closed divs or similar.
could be in one or more of the templates, or in the content of one or more of the latest posts – particular if this happens on the front page and some of the single posts.
