It does look like two small punctures from a bite or scratch. The second lump under the skin could be an abscess if there was any infection passed through the initial wounds. It is normal for a pussy scab to lift in the manner the hair / goo came away, so don't worry about that - It will heal! As recommended, trimming back the hair will let the air at it, and allow you to keep it nice and clean with a dilute salt water or the Hibiscrub solution - Don't be tempted to use TCP or similar, as this is toxic to cats. Warm salt water is always best if you have nothing else - I use a good pinch to a half-pint, and make sure it has fully dissolved, then leave until it feels cool to the finger - not cold.
Keep a close eye on the second lump, as an abscess will burst without much warning! If it does, then you will need to give it a good clean out with the diluted solution, and probably get some antibiotics from the vet. An abscess can be very smelly and pussy, but is nothing too bad as long as it is kept clean. It can appear to be a big hole, but they normally close up with hardly a mark being left.
He will have much much worse as he grows up - Cats get into no end of mischief, and are always snagging claws, fighting, being naughty! It is all part of being a furry family!