I have created a MVC .NET application that has very basic functionality. When I deploy it to my server through IIS and run it within IE, some of the pages do not work properly; by this I mean I am unable to click any buttons on a page and on other pages I have it reading from a file and displaying the contents but this does not work. There are no errors within the console either. When I go to use Chrome or Mozilla to run the application, all the pages work and there is no problems. What server or application settings could be affecting this?
MVC .NET application doesn't work properly in IE but does in Mozilla
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Without knowing a little more about the specific problems you are seeing and the versions of Internet Explorer, Firefox and Chrome that you are running, it's hard to know what's causing your problem for sure.
However, you should be aware that different browsers have different levels of support for JavaScript, and that this may cause differences in how your application behaves. IE 11 has very limited support for ECMA 6, and getting applications that make use of ECMA 6 features run properly in IE often necessitates using a polyfill.
This chart shows different browsers and the JavaScript features that they do or don't support: https://kangax.github.io/compat-table/es6/