There are certain features of the simulator that we're still working on. Any block represented by a pink block with ? on it isn't renderable in the simulator yet. Sometimes, if it's not renderable, nothing will appear at all.
Any badge not in the Skills and Drills section may be too advanced for the Simulator to render. Try testing in Minecraft.
If you've skipped ahead in an advanced level badge, the code may not run correctly at all. With advanced badges, you often need to complete all the badges in order. Herobrine 3 will pull code you've written from Herobrine 2 and 1 by means of the 'Load Starter Code' button at the top of the badge instructions. Also, be patient! The first badges of an Advanced-level badge may not have enough code to produce visible results in Minecraft yet.