Suspect you have not connected the sub correctly. Are you using 1 cable to connect the subwoofer? Or 2 cables?
If using 1 cable, does the connector on the Yamaha you are using for the subwoofer say "Subwoofer" or "Subwoofer 1" or "LFE"? And if the answer to that is "Yes" look at the connection on the subwoofer that the cable is connected to. Does that say "LFE" or "Input"? If not, you aren't connected properly.
Also, if the subwoofer is Bose, it can have weirdness that makes it incompatible with anything but a Bose receiver.
A bad sub could cause the problem, but it would be unlikely that the subwoofer would still sound anything remotely normal if it had a problem that caused it to damage the receiver through an LFE connection.
Another possible problem is that if the subwoofer has a volume control on it, you might have that turned down too low and have the LFE output level on the Yamaha set very high to compensate. That could stress the Yamaha and cause the output to fail. Set all Yamaha LFE settings to NOT add any bass boost (there can be 2 to 4 places where you can adjust bass boost, varies by receiver features) and set the volume control on the subwoofer to the mid-point. When you run the subwoofer test tone, adjust the volume control ON THE SUBWOOFER to get the sub volume to the proper level. This has to be done before you run room correction (with a microphone measuring the sound in your room, if your AVR has that feature).
If using 1 cable, does the connector on the Yamaha you are using for the subwoofer say "Subwoofer" or "Subwoofer 1" or "LFE"? And if the answer to that is "Yes" look at the connection on the subwoofer that the cable is connected to. Does that say "LFE" or "Input"? If not, you aren't connected properly.
Also, if the subwoofer is Bose, it can have weirdness that makes it incompatible with anything but a Bose receiver.
A bad sub could cause the problem, but it would be unlikely that the subwoofer would still sound anything remotely normal if it had a problem that caused it to damage the receiver through an LFE connection.
Another possible problem is that if the subwoofer has a volume control on it, you might have that turned down too low and have the LFE output level on the Yamaha set very high to compensate. That could stress the Yamaha and cause the output to fail. Set all Yamaha LFE settings to NOT add any bass boost (there can be 2 to 4 places where you can adjust bass boost, varies by receiver features) and set the volume control on the subwoofer to the mid-point. When you run the subwoofer test tone, adjust the volume control ON THE SUBWOOFER to get the sub volume to the proper level. This has to be done before you run room correction (with a microphone measuring the sound in your room, if your AVR has that feature).