Minifiers can indeed cause problems as many of them rest on assumptions that will not hold true in every case.
I can really only suggest looking at which scripts are enqueued using the developer tools offered by Chrome, Firefox, IE or some comparable browser and trying to figure out what exceptions you need through a process of test and adjustment, simply because you might exempt one script from minification and find it is still affected by another script that is subtly affected in some other way.
Sorry we can’t do more – and good luck!