It’s not clear what is going on here. Your plan statement by now should not show any non vested balance, but if it does the RMD must be calculated based on the total balance. However, the RMD distributed is paid first from the vested balance and will not include any non vested amounts.
To check your RMD, you need to know the 12/31/2018 plan balance including any non vested amounts that have not been reclaimed by the employer. Then you need to verify that the correct RMD divisor is being used including the reduced RMD if your sole beneficiary is a spouse more than 10 years younger than you. Then determine if the total amount distributed in 2019 meets the correct RMD. If it does not, try to get an explanation of what balance they used and why. Do not worry about any IRS penalty since given the circumstances that the plan is determining your RMD, it the plan is wrong you can get the IRS to waive any penalty by filing Form 5329 explaining the reason.
Since you are long since separated from service, you should be able to withdraw any amount you wish to including the amount you feel is an RMD shortfall. You cannot file the 5329 until you have made up the RMD shortfall. Given all these question, suggest you pose them to the plan administrator.