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The problem has most likely nothing to do with the pipeline but with js syntax of your js files. Consider the following scenario:
// file1.js
var foo='bar'
and
// file2.js
var cat='dog'
When both of the files are separate the browser has no issue processing the js since it automatically can figure out the end of each expression however when you combine and minify the two files you get something like:
//combined.js
var foo='bar' var cat='dog'
The above is clearly a syntax error. So most likely something similar is happening in your case. To solve this make sure that all of the files have absolutely valid js syntax (which is most cases are just missing semicolons).
Source:stackexchange.com