That sounds like expected behaviour... At runtime, class names and package names are scrambled, so stack traces may not look pretty.
Does your obfuscator not have a de-obfuscate function? I imagine it would generate a file with meta-data (mapping between cleartext names and scrambled names) when it does the scrambling.
If your users then have an issue they need support for, they send you their (scrambled) stack trace. You can unscramble that stack trace and make it readable again by using that meta-data file. (You should keep one for every version of your library that you publish.) That's how you would deal with support issues.