"The soft-coated answer would be I feel bad, but I also feel like they just don't go around handing out one-shot penalties here," he told reporters.
"I don't even know of anyone who has ever got one.
"It feels hard to give a 14-year-old a penalty, but he's in the field. He beat a lot of guys yesterday, whatever the age he is."
At the top of the leaderboard, Day will hope to finally end Australia's wait for a Masters Champion.
The 25-year-old finished second in 2011 but produced a sublime round of 68 to ensure his place at the top of the leaderboard.
Tiger Woods had looked set to finish towards the top only for an outrageous piece of misfortune to cost him at the 15th.
The World No.1 hit his third shot onto the par-five 15th only for it to hit the stick and rebound into the pond.
Woods finished on three-under alongside the likes of Jason Dufner, Justin Rose and Australia's Adam Scott amongst others.
Meanwhile, Rory McIlroy will have title aspirations of his own after hitting a two-under 70 to leave him right in the mix.
The 23-year-old, ranked second in the world, carded a level-par round of 72 on Thursday but produced a much improved performance during his second round.
"I made a lot of good putts for pars on the front nine," he told reporters.
"I mean I didn't play my best for the first few holes and the eighth hole (eagle) really got me going, really kick started me.
"Then I started to hit some really good quality shots. I took advantage of a couple of easier holes on the back nine, 13, 14.
"Anything under par today was going to be a good score and I stayed patient out there when I needed to and it was a good day.
"I'm comfortable with my game, I'm happy with this position going into the weekend," he said.
Defending champion Bubba Watson made the cut by the skin of his teeth after carding a one-over 73.
Watson is five-over for the tournament and in a tie for 55th place.
Several big names missed the cut including Ian Poulter, Louis Oosthuizen, Graeme McDowell and three-time major winner Padraig Harrington.