After Gemma and Cady leave the hospital toward the beginning of the film, a wide shot shows them crossing a suspension bridge but the view from inside the car clearly shows they are on a trestle bridge.
At approximately 47 minutes, Lydia hands Cady a tissue and another pops out from the box. The other tissue disappears in the next shot.
At one point M3gan pronounces "either" as "eye-ther", but she later pronounces it as "ee-ther".
At around 1:17, M3gan uses the frame she was suspended from to hoist Cole up off the ground, almost succeeding in hanging him. But this would only be possible if M3gan was heavier than Cole (because the cable was just strung through a simple pulley - a one to one ratio, with no mechanical advantage) And earlier, M3gan was light enough for a 12yo boy to easily carry; Certainly not the same weight as even the lightest adult man.
At 1h27m, a doorknob is pulled out of a door, including the long square shaft that goes in to the opposite doorknob. When the remaining knob is tried, it doesn't turn and seems firmly attached. Without the shaft connecting to its mate, the knob would be able to spin freely without opening the latch, and might even fall right off.
M3gan reads Cady Alice's Adventures in Wonderland, however; the line of Tweedledee's M3gan reads is from Through the Looking-Glass, and What Alice Found There.
The orange supercar M3GAN gets in after leaving the offices is a McLaren 650S. However, when she starts up the car, the dashboard screen displays 675LT, which is a limited edition model released later.
At about 1:00:00, M3gan shoots Celia with a pneumatic nail gun, but the nail gun isn't attached to any source of air.
Nail guns also have safety devices that prevent them from being fired without being against an object.
At 0:37, it can be seen that M3gan's face is not that of a doll.
Right after Cady is bitten by the neighbor's dog Dewey Megan glares at Cecelia over the fence. Megan is not tall enough to look over the fence.
Gemma lives in Seattle, but there are palm trees visible outside her house, which don't grow in the climate there.
Early in the movie Gemma and Cady are driving over the Golden Gate Bridge, which is not only not in Seattle, it's a suspension bridge, of which Seattle has none.
Brandon stabs Cady with a prickly chestnut, but this bangs against plot armor, as it would have given M3GAN a clear motive.
M3gan references Cady's parents dying in a crash on I-84 'outside of Oregon,' which doesn't make sense as Oregon is a state. Someone would either say 'outside of' a city, a different state, Canada or Mexico, or 'off the coast' of somewhere.
M3gan says "You are now my second primary user." Someone can't be both "second" and "primary" (first).