(This point has already been made but i'll elaborate on it a wee bit more) When Darunia enters Volvagia's layer he doesn't use a key, and yet he keeps you out of there with a lock for the boss key.(though maybe he wanted you to get the hammer, but if he did, why just don't leave it at telling you, and when he enters volvagias layer he doesnt have the hammer and doesn't know he is a sage, so he locks himself up for his own DEATH!)
Another point is that you can hookshot onto peoples houses... wearing the iron boots, and walk on their rooftops.
There is a shark in the lake laboratory, when sharks live in saltwater(except for one shark, the bullshark i think, wich can live a short time in rivers, but that doesnt explain how the shark there is living WITHOUT MOVING!, sharks die if they stop moving)
In the fishing pond, the fish start jumping at certain hours(or at least going crazy) because i suppose they are being fed, but no one is feeding them.
Again at the fishing pond, 2 more things, the Hylian Loach appears and dissapears in the tiny fishing pond and the guy managing it doesnt even notice(How the heck can the fish exit and re-enter the fishing pond, he can't get through the mini-waterfall, there is no way back, and the Loach doesn't look capable of swimming back up waterfalls, besides shouldn't the pond owner notice a fish swiming up a mini waterfall? Especially since the fish can weigh from 30 to 35 or more pounds!)
And the last is, how can the fishing pond owner have a big fish (about 15 pounds or more) in such a tiny tank? The fih should have died about a day after you catch it.
Anyways, you may notice i posted a lot from the fishing pond and lake hylia, thats because i love FISH!!!!111!!1!eleven11!