NXP LPC 4330 Microcontroller starts up very hot and sometimes doesn't start up
One possible source of latch-up is USB_VBUS. The datasheet of the LPC43xx allow VBUS to be 5 V only when VCC is present - but in your case this takes a small amount of time until the regulators are fired up. Consider adding a resistor in this path.

Another issue is the ON-Switch of the FPGAs 3V3 LDO. It will be enabled by default, as the GPIO pins are "weak high" when not configured. The resulting voltage level is high enough to switch the regulator on. The SNS pin must be connected to VOUT, if present. You should change the drawing in case they are not.