It may well be that if the medication had such an effect the first time that your E levels are still elevated when you do the second shot. So subjectively you may not experience the same degree of difference. Sort of like how you get a nicotine rush when you first smoke a cigarette but after a while you feel almost nothing no matter how many you smoke. Or to use a non-cancer educing analogy, how some anti-depressants can initially make you feel more depressed but over time make you feel better.
I wouldn't worry about you having missed the muscle. If you did it deep enough it's unlikely, but even if you did, it will still result in increased estrogen in your body, your body will still absorb it, it just may result in different release rates over different periods of time. Just try better next time if you felt you did something wrong, and/or consult your doctor.
Hope this helps.