So at my Work I created a site that when I test it locally on IE9 it works completely fine, but when I upload it to the server of the company, the jquery part is not working properly, what could be the cause of this? and the problem is just with IE9, it works fine in the other browsers

"Not working properly" could be just about anything. Bad mime type / media type settings? File naming rules? Typo in the file name? Script blocking plugins?

What is your exact error?