The agent at your initial check in point probably did put in the backup to protect you in case you didn't make the connection. They're not supposed to finalize it though, so maybe they did made that mistake? Who knows, several different things could have happened, so it's hard to prove anything and determine exactly why the events played out the way they did that night.
I suppose you could try to see if you could squeeze a few flight vouchers, or some miles for your FF account for your trouble, but you're not going to get much more than that. Checks are only cut to passengers when they have been involuntarily denied boarding due to an overbooking situation.
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