The MDATTR specification requires that an entity must have all its entity attributes in one mdattr:EntityAttributes basket. The EntityAttributeFilteringStage relies on this part of the specification by only filtering the first such container.
This means that if there is more than one mdattr:EntityAttributes container, the second and subsequent ones are ignored and left unfiltered. If one is relying on filtering to keep unwanted things out of one's metadata, this is undesirable.
Having the stage throw a processing exception seems overly harsh in this case, and giving it the option of marking the Item with an ErrorStatus would be a significant change to its contract. Combining all entity attributes into one container as a side-effect of EntityAttributeFilteringStage seems likewise out of its scope.
The best remaining approach appears to be to filter each such container independently.