No, it should all go into the carboy, except for the sludge at the bottom! I usually start with 5.25 gallons in the fermenter, and end up with a tad under 5 gallons of finished beer.
I wonder if you started with a 6 gallon kit, and then used a 5 gallon carboy? That's the only thing I can think of that would leave beer left over.
Broken Leg Brewery
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