Can anyone tell me that is there any legal issue involved in using free scripts available on internet i.e if I use one free script today by downloading it from the download link and tomorrow the creator of script comes and ask for penalty as my site is running on his script. Can the creator prove that the script used in a site is his? Can a creator keep track of his script i.e at what all places it is used? Please help me.
It depends on what you mean by free script. Downloaded from the owners site or another he authorized to distribute his script? In other words, an authorized download? Then you would be fine, as long as you stay within any terms, generic or specific, implied or clearly stated. You would just have to prove the authorization, which could well be a screenshot of the download page, a license within the files, and so on.
Read the terms and conditions. Do a research online and in the forums about the script and the script site. If everything looks reasonably OK, you should be fine. To be extrasafe, keep evidence of the results of your research. hotscripts.com is one of the most popular, I believe, there are free and commercial scripts.
Note that if someone offers a script as a "free script," but has no rights to it, you're still liable to copyright infringement by using the script.