One thing to try is cleaning the reference. Make sure the reference is loaded, open the Reference Editor, RMB on the reference, and then File > Clean Up Reference.
Did you group the references manually or using the Group option when creating the reference? Also did you create the reference using namespaces or renaming prefixes? I'd recommend namespaces as renaming prefixes are known to have a lot of problems.
In general referencing has trouble when there is ambiguity over node names, this can happen if your referenced scene has a lot of instances or duplicately named objects, or if you have complex parenting relationships between main scene and referenced nodes. The use of renaming prefixes can also make things tougher for Maya to noodle out.