Oh there are endless possibilities, they might've just put him there to being with when they caught him, since they wanted him and his memories. Then(only a theory) they might've seen him becoming ill or something and had wanted to check him and in their urgency as they realized things were bad, they put him in since they didn't know what to do~ Experts after all><But if Abstergo was putting him into the animus why would they say "He went into shock put him back into the animus" referring that he was already in the animus...