That is why the shops usually do a "flush and fill" for transmissions. There is a lot of fluid that does not drain out of the pan. You probably still had about 6 or 7 quarts of "dirty" fluid in it.
I know some people that don't have the tools to do a full flush will drain it, refill and then drain again to try and get as much of the old fluid out. Then they change the filter after the second draining.
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