Try to use markerGroupRef.current as effect hook dependency.

useEffect(() => {
    if(markerGroupRef.current) {
      //here I want to access a method called getBounds() which is in the markerGroupRef.current object 
      //but markerGroupRef.current has null value and so it doesn't execute
      //when making a save change and react app reloads it has the FeatureGroup class as value as expected
      console.log(markerGroupRef.current)
    }
  }, [markerGroupRef.current])