On the FRDM-K22F board, two of the LED lines were tied to the JTAG TDI and TDO. The debugging is done with SWD, but there is no option in Processor Expert to set the planned debug mode as this is decided at runtime by signal levels on TCLK and TMS. What this means is an inability to use the KSDK along with PE due to the pin_init PinSettings, and no way for PE to not throw errors when adding an fsl_gpio component for the LED lines.
This question is related to: Conflict between JTAG and GPIO pins, using Processor Expert and FRDM-K64F
Unfortunately, PE really should offer some way to handle this! Is there an option I'm missing somewhere?