How do I fix the 3.3V voltage drop on FRDM-KL25Z Board?

The problem is because of Schottky Diode 1. It causes a the voltage of about 0.5V and even larger for higher currents. So the simple fix is to shortcut pin 1 and pin 3 of that diode D1:
Figure 1. Shortcut on D1 of FRDM-KL25Z

Shortcut on D1 of FRDM-KL25Z

That diode D1 is located nearby the KL25Z USB port:
Figure 2. Diode D1 Shortcut Wire Applied

Diode D1 Shortcut Wire Applied

Note: Change the hardware at your own risk. Make sure your power supply is not reverted, and that you only draw a few 100 mA.