The path to the file might be wrong. It could be so many things.
If you want more help:
Please post a link to a page on your site that contains the problematic code so we can check it out.
A word of caution about minifying (if that's what you really mean, it's a technical term referring to the use of jsmin or similar minifying algorithms). Only code that follows some of the strict standards for the placement of the semi-colon and sometimes even brackets will minify well. There are exceptions and this can depend upon the minifying tool used, but it's best to use strict syntax overall. You will end up with a smaller file in the end in most cases, and it will almost always still work - a big plus. See JSLint:
for a tool that will allow you to check and correct any strict syntax errors before minifying.