Something i've been finding funny about some folks on the internet is when-ever they don't understand something they often times shout plot hole. Admittedly M.E.3 has some of these, but reading basic posts about things related to the game that are clearly explained, and they're sill screaming plot hole. People did this with XIII-2 as well. I find this quite interesting.
One thing I definitely don't understand about the ending is how Tali/Liara made it back to the Normandy, and why was Joker using a relay. This I don't get.