I faced the same problem in my website. As you mentioned in your question :
Usually, the Pathauto module doesn't allow to the users to create the node with existing URL by giving the error as "Path already in use"
This is true only when you hand code the URL alias. If "Generate automatic URL alias" box is checked then similar URL's are appended with numbers at the end (like in your case).
The method I used to solve this problem was to install a module called Unique field which makes sure the no 2 nodes have the same title(and thus unique URL for each node).
As for the second part of your question, I didn't understand what you mean. If you could post more info or modify your question, it would be really helpful.