If getReferencedDocuments() is returning NULL for some indexes it means that the alignment does reference any original document for that index. This might be due to a number of reasons. The two most common ones are:
- The user made a change to the alignment and discarded the reference to the original.
- Whatever created the alignment didn't reference any original documents in Geneious
This is still a valid alignment.
If you're creating these alignments yourself then if you tell me how you're creating them or share a code snippet I can provide some advice for including referenced documents if it's applicable.
If you're getting these from elsewhere then it is most likely a valid case that you need to deal with. What are you using the referenced documents for?