Anecdotally I've heard of cases where minifying a script (running through the "uglify2" tool) led to extreme and obvious performance issues (like the UI thread freezing for several beats in cases where unminified JS did not).
In that case, the problem doesn't happen because we are minifying the files, but because this particular implementation of the minifier has a bug. I guess...
In particular, it was only an issue when identifiers were mangled (i.e. made as short as possible).