Not sure why it would start in manual, however it sounds like it was responding to the requirements of auto-gen. If shore power is lost while any of the parameters to start under auto-gen the generator will start and run until that parameter is met. Even if power is restored from the shore connection, if for example the air conditioner is running the generator will continue to run until the air conditioner turns off.
If for some reason your generator "thinks" it is in auto-gen you could go into the settings and disable the settings that tell it to start under auto-gen.