Why are there batteries in the refrigerator of all things? Because cooler temperatures can actually extend battery life. Of course, the refrigerator is not a very good place to store them - since the humidity inside a refrigerator might actually damage the battery.
"Staircase is out of order". It seems like a bit of the game's silly humour - but it might actually not be as weird as one thinks. Perhaps the staircase is actually broken and thus walking up is dangerous.
Meteor Mess (a fan remake) actually fixes this in which Jeff is able to obtain some tools such as a hammer and wooden planks and fix the stairs.
Why does Edna have her own phone line? The only other landline in the house is broken!
While many have interpreted the Publishing Contract ending as the Meteor taking credit for Wendy's work, perhaps all Wendy did was just edit the manuscript into a legible form. These are skills she uses as a member of the college newspaper and presumably a journalism major.
When Dr. Fred sends Purple Tentacle to find an intruder, he's shown in the lab. When he leaves the lab to go catch the intruder, he leaves trough the door that leads into the lab. This means Purple either has a secret passage that bypasses the dungeon, or he's literally going through the dungeon.
