What are the main reasons why javascript and css have so many incompatibility issues in different browsers?
Example: The Javascript and CSS is working perfectly in Web Browser A but have different result in Web Browser B.
Why the W3C allowed different standard in each web browsers?
The W3C doesn't have the power to allow or disallow anything in browser implementations. Different features/bugs/capabilities in different browsers are the product of different companies making their own choices in implementing a browser. The W3C doesn't control what these companies do.
The W3C tries to coordinate a standards effort such that browser implementors will hopefully choose to follow it.
The first thing to look for when you see different behavior in different browsers is a faulty implementation on your part. You may have errors in your own HTML or CSS or javascript that some browsers tolerate and others don't. Or, you may be using some structure that isn't really covered by the standards or is on the edges of what is described by the standards. or, you may be using something that is a particular browser's own addition and isn't widely supported in various browsers.
For example, there are many IE-specific features that other browsers do not support (it worse in IE 9 and earlier, than IE 10).
Here's a partial list of some issues that can lead to cross browser issues: