This is unlikely to be caused by a software error.
Did you also make a $50,000 Qualified Charitable Distribution from another traditional IRA? The $100,000 limit is the maximum permissible for all of the individual's QCDs combined.
Are you married filing jointly, your spouse made a $50,000 QCD and you mistakenly indicated that your spouse's Form 1099-R was your own? If so, correct the entry of your spouse's From 1099-R to show that it belongs to your spouse so that this entry will not reduce the amount of QCD that you are eligible to make.