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What version of sage are you using? It seems that in sage 5.13 that is no longer an issue.

sage: g=graphs.CubeGraph(2)
sage: g.automorphism_group()
Permutation Group with generators [('01','10'), ('00','01')('10','11')]

According to the current code in the automorphism_group method, it seems that the labelling is according to the order given by the vertices method (provided you do not specify a partition as argument).