RRR2 - The Three Doctors 2

In many ways, The Brigadier seems just as dumb and clueless as he did in The Time Monster, but in this story, at least, there's a reason for it. The poor Brig is always in the wrong place when exciting things happen, and is often behind on events when they happen. By the time he is exposed to these events (people disappearing, the TARDIS interior), he is the last person to know.

Not only this, but The Brigadier is much more cynical than, say, Benton. Benton is the first of the UNIT personnel to enter the TARDIS and is, understandably, dumbstruck when he encounters the wonders of the Doctor's time machine. However, Benton is, no offence, less intelligent than his superiors, but he is also smart enough to accept things he doesn't understand. Case in point: Benton's reaction to the Doctor of "Nothing about you surprises me anymore, Doc!". Benton's also lucky enough to experience the sudden appearance of the Second Doctor while the Third Doctor is present. Benton doesn't understand how or why it happened, but it did happen, and, to him, that is enough.

The Brigadier, on the other hand, first sees the TARDIS and can think only of how much of UNIT's resources it took to build and maintain such a thing. He also has yet to see both Doctors in the same room, and so assumes that The Doctor, having changed his appearance before, could probably just as easily change it back. The Brigadier is looking at things logically in this story in a story whose events aren't logical at all. He's looking stupid because he's approaching the problem correctly.