In your attached photo, the brown, shriveled squash shows signs of NOT being pollenated. My guess is that you did not hand-pollenate it correctly - or for some reason, it simply didn't 'take'. The plant seems healthy (based on the photo) so I don't think this was disease. It is impossible to 'over-pollenate' - although perhaps you damaged the stamen when hand-pollenating it. Since squash is very productive, hopefully you have plenty more on the vine to enjoy!
With summer squash, pick as soon as the plant is a good size to eat - I'd say 6"-8"; they can immediately be eaten. Late in the season, the vine will naturally start to die off. With winter squash, pick fruit off the vine when the squash surface is hard enough that you can't puncture it with a fingernail. Then let winter squash cure ("sit" - many let it sit in the field; I put mine on my porch) for 10-14 days, then store in a cool spot (about 50 degrees) for optimum storage life.