The Wordof God is that it was originally just a dream. Guybrush ran off to play Pirates and Chuckie was sent after him. The whole thing took place in Not!Disneyland, hence the Treasure of Big Whoop being an E-Ticket (Disneyland used to use a graded ticket system with E-Tickets earning access to the most popular attractions). LucasArts wasn't satisfied with this because it ruled out further sequels, so the ending was changed. Chuckie's evil/possessed look was added, along with Elaine's line about hoping Guybrush isn't the victim of a horrible Voodoo spell.
LeChuck may have arrived during those three days Guybrush spent hanging inside the pit.
How did Guybrush's parents die? Or, if their skeletons are just part of LeChuck's spell, what did LeChuck want Guybrush to think? That his parents went to the lost property office, and then just sat there until they starved to death?
Assuming the whole game is All Just a Dream, Guybrush needed the last part of the voodoo doll to defeat his evil brother, so he simply pretended that a pair of prop skeletons were his parents. That, or LeChuck murdered them and hid their bodies there.
How did LeChuck get the materials for the Voodoo doll in LeChuck's Revenge anyways? We never see him get the materials for it.
Presumably, he has the "something of the dead" from Guybrush's parents. He states that the rest of his ingredients are flawed, as his doll only teleports Guybrush to the next room, as opposed to a dimension of pain.
For the thread he used the pink dress, for the body he used spit, and for the dead he used his parents. As for the head... well, maybe he used hair that fell off when Guybrush scratched his beard?
If LeChuck flew into the sky and exploded, how did Guybrush manage to find his beard? Why didn't Largo take the beard the first time he robbed Guybrush? And why didn't Guybrush use the Largo voodoo doll to get the beard back?
What's the deal with Wally's visual impairment? In Revenge, he only has a monocle on his left eye, and becomes blind upon losing it, but in Curse, he has an eyepatch on his left eye and can see just fine. If his right eye works perfectly, why didn't he just close his left eye in order to see better?
Why did LeChuck make a voodoo doll of Guybrush if he was going to drop him in a pool of acid?
Why didn't Elaine climb down the pit to help Guybrush, but instead just stood next to the hole, waiting for Guybrush to somehow climb back out after falling hundreds of meters, possibly into a pile of smashed rocks, and definitely into the hands of LeChuck? And how did she know LeChuck was down there anyway?
If Blondebeard didn't have any chicken, how was he able to serve a value meal to LeChuck? Sure, maybe he used ipecac slaw instead of super slaw, but where did he get the drumsticks?
In the 4th game, talking to Cheese at the SCUMM Bar implies that he is able to beat Ozzie Mandrill at Insult Arm Wrestling. And yet, he is pretty much a pushover who Guybrush can beat without trouble? But then you can swordfight Ozzie later and he's so good that the fight is unwinnable?
What exactly were LeChuck and Largo doing to try to stop Guybrush from completing the map to Big Whoop? Largo somehow finds out whenever Guybrush finds a map piece, but doesn't try to capture him, presumably because of Guybrush's voodoo doll. LeChuck states that he searched every island for Guybrush, but apparently forgot to check the three islands where the map pieces are hidden. Did they ever even leave the fortress?
Stan somehow knows Guybrush's real name, but doesn't seem to care that Guybrush cashes in his life insurance under a false name. What gives?