Are there any know problems when Web pages using .js files?

I would like to know if there are any known problems with Web browsers and 
other assistive technologies (e.g., JAWS) with external JavaScript files 
(assuming the browser has JavaScript enabled). I know JavaScript shouldn't 
be important for people who can't have JavaScript in their Web browsers, 
screen readers, etc. I try to avoid fancy features with JavaScript 
(basically, the Web pages are usable without these features).

Thank you in advance. :)

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