The brown spots, or you may see them as orange or reddish-orange, are where the egg touched the hot tin while baking in the muffin pan in the oven. Nothing is wrong with the egg. It's still good to eat. You can remove the brown spot if it bothers you. We did a test to see which technique worked the best to eliminate the brown spots. On one side of the muffin pan, we put a single cupcake holder in one of the cups and 2 cupcake holders in another cup and laid an egg in each one. Then we put heavy-duty aluminum foil on the other side of the muffin pan and laid the eggs on the aluminum foil. We baked them for the same amount of temperature and time - 325 degrees Fahrenheit for 30 minutes. Test Results - both the single-layer cupcake holder and the double-layer cupcake holder produced a brown spot on each of the eggs. The aluminum foil did not produce a brown spot on the eggs, except a tiny spot on the outer membrane of one egg. We also tested this on a silicone muffin tray and there were no brown spots on the eggs. So if the brown spots bother you, you can use aluminum foil or buy a silicone muffin tray. I have read that you can use a casserole dish, but I have not tried that yet. If you have, let me know how it worked out.