Muffins are currently only earned by unlocking achievements. Originally they were going to be a prestige reward as well, but that feature’s been disabled for now. The amount of muffins earned varies with the achievement; generally, the first achievement for each building type is worth one and each one thereafter is worth one more than the last.  
Buildings can be sold by right-clicking on the appropriate button. (If your device doesn’t support right-clicking, do whatever normally opens your browser’s context menu) You can buy or sell buildings ten at a time by holding Shift as you click.  
There are a number of non-obvious actions in the game that have achievements attached:  

• Save the game manually.  
• Export a save.  
• Import a save.  
• Click the pony on the credits page.  
• Start the Smile Song from the menu.  
• Sell a friendship. You monster.

1. The game refuses to fit to my screen.  
2. Every time you add another pony one or several friendships are broken.