It happened to me several years ago on a United flight out of IAD. I arrived 90 minutes early and discovered that for some reason they had Christmas level crowds in August. After a very long time in the check in queue, I arrived at the counter something like 4 minutes after the cutoff time and they refused to check me in. No compensation and they also treated me like I was a poor planner who'd just waltzed in expecting to get on the plane on a minute's notice. Even the call center (the desk agent's only help was to point at the phone handset that direct-dials the call center) would not budge.

I had to rebook for the next day's flight and showed up at my client's site a day late. That didn't impress my boss at all. Ever since then I check in online the day before.