*The Normandy is seen fleeing from the battle it was taking part in, through a Mass Relay, and it appears at a random planet, where it crashes. Why would Joker flee?
*Squad members are shown departing from the Normandy, even those that were with you during the battle on earth. How did they magically teleport back onboard the Normandy?
* Every alien race, along with the entire Quarian Flotilla, are now stuck in the Sol system. And earth looks like it is barely in any state to support life for just humans. How the hell will anyone survive all that?
* The explanation given by the God child is basically just one big line of circle reasoning, and not an explanation at all.
* Why would the Mass Relays be destroyed anyway, regardless of what ending you choose?
* How the hell did they get the Citadel to earth?