Farheen, I’m reporting a bug, not asking about how to do something. When you assign a term to a post, the count field in the term is incremented by one (I’m not talking about the ID field, terms has another field called count). That field track the number of times a term has been assigned to a post. That’s a normal behavior of WordPress with the included post type and the categories and tags taxonomies.
When you create a custom post and a custom taxonomy and make a relation between them using Meta Box, all work as expected, except if you use the plugin MB Custom Table. With a custom table, the field count doesn’t increment when you assign a term to a post.