Hi bilekas,
That could be a problem, but it could be done in the last step, once the theme is finished...
I think that also Chrome offer you he possibility to "follow" the code, If you click or doubleclick on the error, it send you directly to that line of code (on the combined file) which doesn't solve the issue but could help you know the real location of it.
This also happen if you use "minified" versions of the scripts...