Well, let's think about this, why are only humans used for the harvesting power?
Where are all the organisms? You know the ones that don't need the sun.
Morpheus: A singular consciousness that spawned an entire race of machines. We don't know who struck first - us, or them. But we know it was us that scorched the sky. At the time they were dependent on solar power and it was believed that they would be unable to survive without an energy source as abundant as the sun.
One could say that all organisms became extinct? But that's stretching it. The machines must have been smart enough to take some organisms with them and mass produce. Just based on logistics, you would be able to save on computing power to run the simulation. Seriously, the amount of 3D rendering that goes on in the Matrix must be a lot
Next part, everyone is all on the ship training Neo to be the one and all that so after Cypher talks to Neo and gives him the drink on the ship how in the world did he boot into the Matrix for dinner with Mr.Smith?
Was it someone else? No, because Cypher was on shift that night to monitor code on the Matrix. So let's say he managed to get in. Who got him out?
There are many more holes, I will have to watch it again to remember. Notice, this is all based on the first movie.