There are a few main reasons why this warning message occurs. It's important to keep in mind that Sphere plug-in is designed to only work on 2-channel audio recorded with the Sphere L22 microphone. If you are feeding mono audio tracks recorded with some other microphone, then the warning message is expected and designed to flag that an incorrect source is being used.
This can also happen because the Sphere plug-in is processing audio which was already processed. When using the UAD Sphere plug-in this can happen in the UA Console application if using UAD REC mode and the Sphere plug-in is also used to process the same audio channel in your DAW. Instead, use UAD MON mode, so the processed audio is not recorded.
Another reason the message can occur is when the "CAL" switch is enabled on the Sphere microphone, which is used to calibrate your preamp levels. When in CAL mode the Sphere microphone outputs the identical signal on both channels. But once the preamp levels are adjusted to match then the switch should be moved from the "CAL" position back to the "ON" position, meaning that the microphone is in normal operating mode. If the microphone is left in the CAL position then the Sphere microphone modeling will not work properly.