This one has annoyed me for years: Unity’s OnMouseDown has never really worked. (NB: it works perfectly if you make a scene with a single cube; but that is not a game. It breaks completely as soon as you add multiple objects, colliders, etc to a scene)
The main reason to use a 3rd party engine is to avoid re-inventing the wheel; it’s tragic that Unity can’t even do mouse-input out of the box. Let’s fix it!