Answer
In the Name of Allah, Most Gracious, Most Merciful.
All praise and thanks are due to Allah, and peace and blessings be upon His Messenger.
In this fatwa:
Burying Muslims in mass graves along with non-Muslims can only be done for the sake of necessity.
Answering your question, Dr. Jasser Auda, Professor and Al-Shatibi Chair of Maqasid Studies at the International Peace College South Africa, states:
Burying Muslims in mass graves along with non-Muslims depends on the context. If there is a necessity and Muslim scholars in the region assess that Muslims can be buried in mass graves along with non-Muslims, then there is nothing wrong with that. Otherwise, there is no general rule for such things as they depend on the circumstances.
Almighty Allah knows best.