"Machinima" is computer animation, but it isn't. Machinima is specifically using a game engine to create scenes and movies, such as My Little Derpy (uses a GBA emulator) or Red Vs. Blue. RvB used to use captured footage from the Halo games, but now, they have 3D models and it is more traditionally computer animated. Cut scenes in video games are technically machinima because they are using the game engine. Those of you who saw the alpha for the Doctor Whooves game I made know what I'm talking about.
This also means that 12 Oz. Mouse and Spodermen are computer animated, as the creators used or use, respectively, Final Cut Pro to make the shows, even if Spodermen doesn't really have any animation at all.
Basically, don't think about it to much, just roll with these general definitions or your brain will explode.