That's like saying Kurama was never sealed in the Shikigami. Part of him got sealed other part didn't, simple as that.Orochimaru was never sealed in Totsuka to begin with, he escaped at the last second.
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Those three snakes then slither off, preumably carrying Orochimaru's consciousness. We know one of them died when the flames of Amaterasu fell on it. The other two must have died at some point as well, because Orochimaru's consciousness transferred to Anko's Curse Mark, where Sasuke released him.