They were never allies. They had a pact together to fight the Whites which was well-known between both sides to be temporary.

Upon the signing of the pact, Makhno had this to say in The Road to Freedom, the publication that was the Makhnovist mouthpiece, on October 13, 1920:

"Military hostilities between the Makhnovist revolutionary insurgents and the Red Army have ceased.

Misunderstandings, vagueness and inaccuracies have grown up around this truce: it is said that Makhno has repented of his anti-Bolshevik acts, that he has recognized the soviet authorities, etc. How are we to understand, what construction are we to place upon this peace agreement?

What is very clear already is that no intercourse of ideas, and no collaboration with the soviet authorities and no formal recognition of these has been or can be possible. We have always been irreconcilable enemies, at the level of ideas, of the party of the Bolshevik-communists. We have never acknowledged any authorities and in the present instance we cannot acknowledge the soviet authorities. So again we remind and yet again we emphasize that, whether deliberately or through misapprehension, there must be no confusion of military intercourse in the wake of the danger threatening the revolution with any crossing-over, 'fusion' or recognition of the soviet authorities, which cannot have been and cannot ever be the case."

Those are not the words of allies and, regardless, you don't sign pacts with your allies.

This anarchist historical revisionist myth (along with the persecution fetish such arguments furnish) needs to die its long-overdue death but it won't because anarchism is the highest stage of not doing the reading.