We can say that if there is no way to have separate graves for Muslims in such situations, then there is nothing wrong with Muslims being buried in a mass grave that includes Muslims and non-Muslims.
Dr. Rif`at Fawzi, former professor of Shari`ah at Cairo University, states the following: First of all, I would like to stress that Muslims who died in such devastating human disasters are considered martyrs. The Prophet (peace and blessings be upon him) is reported to have defined a martyr as, “One who dies in a plague, one who dies of intestinal ailments, one who dies of drowning, one who dies under a collapsed building, and one who dies as a martyr in jihad.” Thus, those who die in such afflicted areas are martyrs.

Moreover, the Muslims who die there should be hurriedly buried in a Muslim graveyard, if possible. If it happens that the corpses of Muslims got mixed along with the corpses of non-Muslims in a mass grave, then there is nothing wrong with that, as burial in this case is nothing but covering the dead body.
here, I should make a distinction between what maybe termed as a “physical grave” and an “abstract” one; the physical grave here is the mass grave where Muslims are buried along with non-Muslims, but the abstract one is the grave where each one will be either rewarded or punished according to his deeds in this world. The last concept, reward and punishment in al-barzakh or life in the grave, is known to almost all Muslims.

Moreover, the eminent Muslim scholar and renowned Egyptian da`iyahSheikh `Abdel Khaliq Hasan Ash-Shareef adds: If there is no way to separate the corpses of Muslims in such a situation, and the corpses of Muslim are buried in a mass grave along with non-Muslims, then there is nothing wrong in burying the dead Muslims in a mass grave.

Finally, Dr. Sano Koutoub Moustapha, professor of fiqh and its principles at the International Islamic University, Malaysia, concludes: Those who die in such disasters should be shrouded with whatever is available. There shouldn’t be any worry about any mixture with others.

If they fail to even find a shroud for them or they shroud them with others, there is no problem. Thus, their souls have already been taken and they are living different lives in Paradise, in sha’ Allah.