Do you leave anything in the crate for him to chew? Definitely keep in mind that chewing helps trigger defication and younger dogs are definitely less prone to hold it in. My boxer ate his backyard bombs a few times when he was young better never has since. I think there was something you could feed your dog that made them less likely to eat their poop. Can't remember what it was.
Like any bad habit for a young dog I'm sure there is a good chance that he will grow out of it.
P.S. I feel you on as far as your wife making the discovery. I've been read the riot act a couple of times.
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