1-It's possible that you placed the child just a few seconds before the mushroom was to wilt away. This is a '_bug_' that is in the game where the mushroom is still visible when it is not pickable anymore.

2-Once you've finished all the building projects there is no need to keep a builder so yes, having pop 90 w/ no builder is not abnormal. You can however still train builders after building projects have been completed but all the will do is 'fixing hut'. The huts will not fall in disrepair if you don't 'fix' them though, it's just a way for you to keep builders if you want 'em.
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If you always do what you always did, you always get what you always got.