(This) happened to me several months ago, when an assistant and I traded emails at a NY literary agency. They loved the query; "send us your first chapter." They loved the first chapter or so I was told; "send us your full." The next day, I received an email, "Sorry, but we found the writing confusing, best wishes, etc." I was printing the last section of the full manuscript at that moment. Really can't describe the haze of the next five minutes, but I remember some use of colorful language was involved.
This is one of the few cases where I would actually recommend contacting the agency to ask what happened, because this sounds like a case of miscommunication.
For the most part, assistants do not request partials. Agents do. I can only remember one or two instances where I nudged an agent into requesting a partial when he/she didn't want to, and it ended ultimately in rejection for that person.
My guess here - and this is a real guess - is that the second email was a mistake email. We try not to do it, but it happens. Envelopes get stuffed with rejection letters when they shouldn't, SASEs get lost, the agent hits the auto-reject reply button on her mail program to the wrong email. I always double-check that the name on the query matches the name on the envelope of the person I'm rejecting, but I'm human. In our office there's a stack of mysterious SASEs that don't seem to have matched any query letter we had. Everyone screws up at their job once in a while, including agents and their assistants.
If you queried multiple agents with a good letter, you should get more than one positive reply, so it shouldn't be a huge worry. If you tell me you queried 100 agents and this was the only positive, I would say something's wrong with your material. So one screw up at one agency is not going to mean that you will never get published. And if you have reason to believe there was a mistake made because something just doesn't make sense, feel free to email the agency. We're incredibly apologetic about these sorts of things because we feel bad about them.