Auto-discovery uses reflection on all assemblies found in-scope. This might be a problem if the assembly is for example obfuscated or not 'reflectable' (is that a word? ).
If auto-discovery gives problems like these (and the auto-discovery process can only know if an assembly has injectables if it has analyzed it so this exception is unavoidable in some situations), you've to specify the assemblies manually. there's nothing wrong with specifying them, as it's also in general faster.