The reason Weasel and Baboon ended up with the others brain is because the doctors that operated on them were ignorant and believed that the size of their had matched the size of their brains.
It seems that at this point, it wasn't confirmed that i Am Weasel was going to return along with Cow & Chicken, therefore, the writers made this episode look like a finale for the series. However, the series was renewed (with a couple of changes, see next episode's NOTE) and they didn't bother with continuity, as next season, Weasel and I.R. got their brains back, which could be considered Non-canon.
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