You have a Klipper version running on your RPi (which is recent) AND ONLY this version can be updated via the Update Manager in the webinterface.
Then you have the Klipper parts that are running on OR as a MCU. This can be the additional MCU process on the RPi as per RPi microcontroller - Klipper documentation and the Klipper parts on your printer board. They CANNOT be updated via the Update Manage since you need to run a make menuconfig
This error message notifies you that these versions are too old. You need to rebuild / reflash
In general this is a good message, since it shows that we are one step further and Klipper does no longer error out already at checking your config
Edit:
Also see Klipper Architecture / Ecosystem for a bit of background knowledge