I'm not totally clear on what you mean. Do you mean that you've only hatched one egg today, and somehow the two other hatches vanished with it?
A while back there was an issue with the Hatchery sometimes taking hatches (usually only one), but that was before the Hatchery revamp and I haven't heard of any sort of problems since.
Maybe you hatched the other two right after reset the day before, went to sleep, then woke up and hatched one? Reset goes by res time, not real world time, so perhaps that's what happened?
Or did you switch to merchant? Merchants only get one hatch. Ranchers get three. :U
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