Ahhh, now I get it. You've got multiple things that can beep, and may not know for sure what's beeping either. In my experience (not including big Yammies), big outboard electrical systems have a remote beeper module that is often mounted at the console. Many boat companies just tie it up in the wiring harness under the dash. So, even though your outboard may beep at you, expect that the sound will come from somewhere around the driver console, not the engine itself.
For my brand motor, a problem can trigger the motor to limit the RPM intentionally in an attempt to prevent me from blowing the motor. Yours may have been doing that when you noticed it would not run over a certain RPM. It's trying to say "I'm not sure what's going on, so be careful with me." Maybe some Yamaha guys can give you more info. Be sure to post your exact model for better help.