It not that an uncommon scenario that two transformers (same src and dst) get registered in mule.
When such a thing happens and a transformation is needed mule just fails.
This could happen either because, to jars (different version) containing the same transformer got loaded into the classpath or because during init a transformer bean want's to register itself.
What ever the reason, Mule should prevent this from happening either avoiding the registration or allowing it and afterwards deciding which transformer to use deciding itself instead of just failing.
If possible mule should expose a way for the end user to specify how to resolve such conflicts.