recently i saw a bookmarking website which has pr 6 but i checked backlinks it has only 3 backlinks from pr 2 website. site doesn't have original content also. i dont no how google calculates pr
Try to check backlinks with the help of another tool. Sometimes the tools are wrong and show irrelevant results, e.g. less backlinks that link to the website given.
The owner might have bought an old, expired domain and link it to this "crappy" site that you're describing. No one, except Google, knows how PR is calculated because its algorithm is always changing.
It is really a strange thing. I think you should have to try another tool for checking back links of this site. Make sure what are exact back link of this site with the help of more than two tools. So, that you can get perfect result. On the basis of which we all can suggest you further..
I have experienced same problem, I bought an expired domain name which has page rank 5, I checked its backlink using backlinkwatch.com, it doesn't show any backlink, but I used other tool megistic something, it is showing many quality backlinks so it depends on backlink checker.
Use ahrefs to check the backlinks and get a overview of you backlink profile. It has a free version that works well for quick overview. http://ahrefs.com