I think the biggest mistake you can make is shifting your mindset from making a game to making a game engine. No, you still want to be dead set on making your game, you just don't have the ready-made building blocks from an off-the-shelf engine, so you have to make your own as you go, and only as needed. Personally, when I was working on my little game, I found it helpful to call the endeavour—just like Noel Berry in TFA—"making a game without an engine", rather than "making a custom game engine". I only really wrote the absolutely necessary plumbing that I needed for the game I was making, nothing more.

The same goes for software libraries in general, I think. Just make your program. Don't make an overly general library for something you won't need anyway. If the code proves useful for reuse, just factor it out after the fact and generalize as needed.

EDIT: Typos, wording