You didn’t miss some secret flying rule.
People check backpacks all the time, especially larger travel backpacks that are basically soft suitcases with straps. As long as it’s tagged properly, it can go in the hold like anything else.
The only real issue with backpacks is:
Loose straps can get caught in belts if they’re not secured
People sometimes forget lithium batteries inside
That’s it. There’s no etiquette rule that says “backpacks must stay in cabin.”
It sounds like the staff member was just stressed because they had to dig your bag back out at the gate, and the backpack comment was more frustration than policy.
You already learned the battery lesson, which is the only actual safety thing here. Beyond that, checking a backpack is completely normal.
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