The gpio pins have low tolerance. Apply more than the 8mA or 3.3v and you permanently damage your board. LED's usually require 20mA to achieve a good brightness so you have to create a safe circuit using a bipolar transistor and the 3.3v power pin which supplies way more current than a gpio pin. If you hook up that transistor wrong or short the circuit it's game over.

I actually think you can even damage the board if you create a short between the gpio pins and ground. So any kind of circuit requires a resistor, carefully reading the system manual and data sheets for your components and using ohm's law prior to hooking up components.

Our team has personally blown through three of them through shorting faults. It's our fault, but the BBB is a pretty tender beast.