Tim, I don't see any design flaws. I normally tell people to provide easy access to land when it comes to water features, and you did. But they also use the glass to climb out. So I doubt it's a water depth issue.
You said you added plants, any chance they got tangled up in them, preventing them from getting out?
Aside from that, I would test your remaining animals (obviously not the crabs or fish) for diseases/parasites.
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