There are HUNDREDS of plotholes and questions those final 10 minutes introduced. If they really want to stick to the current, extremely nonsensical endings, they're going to need at least a few hours to go down the list of grievances one by one.
Why did my teammates teleport onto the Normandy? Is the explosion different than from Arrival and what the in-game Codex says it is? How did Anderson beat me to the Catalyst? Where was the Illusive Man hiding and how did he get there? How did he get those new powers we've never seen before? Why does the Catalyst look like a dead kid? Why can't I question the kid at all? Why can't I poke holes in his nonsensical logic that I've PROVEN to be wrong in the past? If I die in the Control ending, how do I control them? Am I a ghost? What's stopping them from coming right back or ignoring my control? How does Shepard possibly survive in the Destroy ending? How does Synthesize even work? Did I just turn trees into robot trees and toasters into people? How are all those billions of soldiers stranded over earth going to survive? How can turians and quarians survive if they can't even eat our food? Why was every choice I made in the game negated and made meaningless? Did the people on the Citadel survive? Like Kelly, or Conrad, Liara's father, Ashley's sister, or Dr. Michel? Why does the Destroy ending kill geth and EDI too? Why can't it just kill the Reapers? What happens to the millions of husks, brutes, banshees, marauders, and cannibals left on earth in two of the three endings? How come Harbinger leaves after blasting me in the face with his death beam? What happens to all those colonies and space stations that are now stranded without mass relays for food and supplies? If the energy beam from the relays WASN'T destructive, how was it destroying the Normandy? Why was Joker fleeing the battle in the first place? How did Joker survive the crash without a single bone being broken when he can't even sneeze hard for fear of breaking a rib? How on earth can the Normandy crew survive on a desolate planet and repopulate? What was going on with Liara's weird dream/memory at the end? Why did my Shepard even see her in visions in the ending instead of his/her actual love interest? How did Shepard, who could barely stand and walk, suddenly get the strength to just start running full speed towards the end of the game in Synthesis? Why does the Catalyst even have those three options present at the end? Why would the Catalyst allow two of the three choices to destroy itself so willingly? If I picked Destroy, which kills all synthetics, does that mean I killed Kaiden, Tali, Garrus, Jack, and all augmented biotics or people with biotic implants, which are synthetic technology in their very brains? How can earth support billions of alien life forms when it looks like it can barely support its own? Did I just kill more people than the entire Reaper fleet combined? If the Citadel just exploded over earth, isn't it going to crash into earth and cause a new Ice Age? What happens to the trillions of now homeless, wandering people I've just stranded over earth, from both fleets and refugees from the Citadel? How can Synthesis even work on a genetic level if Synthetics don't have DNA in the first place? Why did the game basically turn into a game of "Choose Your War Crime" devoid of any Paragon choices whatsoever? If Starchild was in the Citadel the whole time, why did it need Sovereign at all in Mass Effect 1?
I know Bioware is at least TRYING. They may be trying in the wrong direction, but at least they're trying. Props to them for that... though if they want to give true clarity, they're in trouble.
They introduced more plotholes in the final ten minutes than there was actual story in the entire three games combined. It might take a whole 'nother game just to "clarify" every problem the ending introduced.