The game takes place in its own universe
- The game is neither in the Aligned continuity,nor the Bayverse. This explains why Megatron looks like Fall of Cybertron Megatron, even though he didn't have this design yet. It also explains the movieverse being a major part of the game.
Some of the differences between the Movie portions and the actual Age of Extinction could plausibly be explained as follows.
- Since the Autobots are just there in the city with no human opposition and still concerned for them, the movie portions likely take place shortly after Dark of the Moon, but years before Age of Extinction. The anti-Transformer sentiments regarding the Battle of Chicago probably took a while to dawn and sink in on people, like any mass hatred towards any group for any reason.
- Lockdown's shifting characterization between this game and the movie could have been Quintessa brainwashing him, like she would with Optimus. The lack of a glowing scar on Lockdown can be chalked up to The Last Knight not being thought up yet, and the staff of the movie not finding adherence to this tie-in game a big priority.
- Also, Lockdown not knowing Megatron wasn't really dead- the Autobots didn't know, either, and construction on Galvatron only began when KSI obtained and tinkered with his parts. Plus, Lockdown was working with Attinger, not with Joyce (who didn't even know about Lockdown). However, this still leaves the plothole of Stinger's dual existence in Lockdown's mercenaries and as a KSI invention.
- Optimus and Bumblebee already having their Age of Extinction designs could either be artistic license to strengthen the tie-in with the movie, or they just scanned the new alts after Dark of the Moon, scanned a different look after Cemetery Wind was formed, and re-rescanned the new movie cars.
- The Autobots' pre-existing alliance with the Dinobots could be explained as the opening scene of Age of Extinction taking place in the years between movies and the 'bots breaking free of their icy prison. From the cutscenes, it's discernible the intent for Grimlock chasing off the mercenaries was giving a window of opportunity for him and the other dinos' capture.
- Regarding Optimus' Cybertronian comment to Grimlock when freeing him in the movie ("The legend exists"), Optimus had been locked in that room with the Dinobots for a few hours, so he already knew the Dinobots were there. The comment was probably to re-assure the big rex, since if Optimus was legit surprised, he would have said the comment in English to himself, not in Cybertronian to Grimlock. As for Grimlock not being willing to let Optimus ride him, Lockdown had likely kept the Dinobots in captivity for years with no rescue from Optimus, and likely with no knowledge of Cemetery Wind's existence or hunt for all Transformers. Plus, you just don't ask to ride someone and expect a quick okay. The only hole, though, is Drift's otherwise funny joke on Grimlock's alt mode from Age of Extinction.