Url adds zero at the end and duplicate contents appearing
This is a common way how url aliases are generated - if there are nodes with the same title, it appends the "0" (and "1", "2" for more duplicates). 

So if you really need nodes with duplicate title, you can edit the path alias manually on node edit form to something else. But from the seo point of view, its not a good practice to have multiple pages with same title. 

The best option in my opinion is to avoid such duplicates completely. For your situation, you can use Remove Duplicates module to delete duplicate nodes based on the node title.
(For drupal 6, you have to do some coding - here)

One more idea: if the case is that you have multiple content types and you need two nodes of different types to have the same title, change the alias rules so that different types have different urls (e.g. blog/my-title and article/my-title)