There was a game played with New Caprica and it had a Cylon was infiltrating. Throughout the Corse of the game every person ended up in the brig at the same time, except for the infiltrating cylon. The Cylon can not be admiral and the admiral can’t be in the brig. Who becomes the admiral?

I told the group that the person getting tossed in the brig would lose the admiral title and it would go to the highest person in the brig. Any thoughts?

It's in the FAQ. If all elegible people are in the Brig, the highest of them on the list of succession becomes the Admiral.

As soon as someone leaves the Brig, that person becomes the Admiral instead.