For some reason when I extrude the pentagon, it also extrudes on the Z axis and not just on the X and Y axis. Can't figure out what I'm doing that's different from the video. Doing E +S and dragging and it's just changing Z height on it's own.
Doing a temporary fix and just moving them back to the correct plane by hand, but it would be good to know why it was doing it in the first place!
I think I can reproduce your issue if I change the Transform Pivot Point to "3D Cursor",
3D Cursor
I believe you want it to be "Individual Origins"
Individual Origins
If you want to make absolutely sure it's scaling in the axes you want, you can constrain it by Shift + the axis you do not want to scale in, e.g. if I want to scale in XY and not Z, I would press S and then Shift + Z. It also works for the other transforms, too.