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doghouse
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This expression may be a railroad term dating back to the early era of steam locomotives. The railroad unions mandated that a head-end (front of the train) brakeman be so positioned. However, there was no room for another person in the engine cab (which housed the engineer and fireman). The railroads then built a small windowed shelter on top of the engine tender (where the coal and water was stored) behind the engine. It was called a doghouse since it was small, cramped, smoky, cold and generally miserable. Thus, the expression 'he's in the doghouse' referred to the brakeman in his uncomfortable moving shack...
Apart from the fact that a doghouse was a kennel or a railroad caboose, as earlier answers suggest, the phrase itself - "in the doghouse" (in the sense of 'in trouble/disgrace') - is relatively recent.
There is no record of it in writing anywhere prior to the 1930s. No 19th century dog-owner and no 20th century railwayman was ever said to be 'in the doghouse' in a figurative sense, though they may very well have been in a literal sense!