Paid an extra "late fee" because I cant get boarding pass even when I checked in.

I checked in last night and no boarding pass on my phone today when I was at the gate??
It says here on their stupid website that I have to go back to check in at the counter. They said I have checked in but was late for the gate.
Why? BecauseTHEIR LOVELY WEBSITE told me to.
And an extra $75 to get on another flight. Beauty!