Yes, this 12-minute video expertly dissects all of the inconsistencies, logical fallacies and plot conveniences that plague 1999's The Matrix. But what it fails to take into consideration is that The Matrix is perfect, and no amount of nitpicking will ever change that.
Yes there are problem spots if you want to look at Neo's journey under microscope (or maybe just a zoom lens). But but but: bullet time! Red pill/blue pill! Agent Smith! I know kung fu! These are parts that add up to a sum that is perfection, end of argument. Go quibble with some other patsy, CinemaSins! You'll find no sympathy here.
As for flaws in The Matrix: Reloaded and The Matrix: Revolutions, well, it would be easier to just make a video of what in those actually makes sense.