Factual error: The elevator Cade leaves because there's "too much weight" shows in the next scene a weight limit of 680kg. Even if the four passengers weighed 90kg each (a total of 360kg) it would mean the seed weighed more than 320kg (over 700lb), which would mean that Joyce would never be able to carry it alone as he did several times.
Factual error: Once they escape the large ship, the humans and Bee hop on the ship Crosshairs is piloting, and they take off through the city, being chased by three enemy ships. Bumblebee, standing on the back of their ship, shoots a grapple hook at a good sized fishing boat and then flings it up into the path of the enemy ships, destroying one. But this is where physics fails. The ship they are in is not affected by this action at all, yet Bee is standing on it and uses brute force to lift a heavy object into the path of an identical ship very swiftly, and the ship they are on does not even get fazed by the action. At the very least, the ship should have suddenly bucked down in altitude from the sudden additional weight of the ship Bee grappled and pulled on, having a effect similar to an anchor, as well as Bee's motion in jerking it upwards really fast, having an equal and opposite reaction to the ship he is standing on.
Factual error: Darcy tells Joshua Joyce about the meteorite that caused the dinosaurs to become extinct; she mentions that the piece of metal in question has been carbon dated to 65,000,000 BC. Carbon dating is limited to around 40,000 years. For longer time periods potassium-argon dating or other techniques are used. Additionally, carbon dating is used for life forms, not for metal.