Believe me it is possible to raise more than 3 in a phoebe nest. We have lots of phoebes, and one time I believe they had 5, it was definitely stuffed though!
About your egg question, not quite sure about that, but I know a lot of birds lay one a day and don't start incubating until all the eggs have been lain (for obvious reasons, if they incubate starting with the first egg, then they will have a stair step of ages with the babies). So perhaps your bird was still laying when you left which would explain why they haven't hatched.
Hope this helps!
featherbrain
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