"Do you have any advice on how to fix the problem? "
No, I haven't used that tool recently and I can't guess at all the facts you entered. Be aware the lifetime learning credit is 20% of tuition up to $10,000 (up to $2000 of credit), but can't be more than the tax liability. I would run the estimator without trying to enter the LLC, and see what his tax liability (obligation) is expected to be, and then consider the LLC separately, manually. For example, if his obligation is $2078, then his LLC will be 20% of tuition up to the maximum of $2000 (meaning, if he pays more than $10,000 of tuition, he would get the max LLC of $2000 and his net tax owed would be $78. Or if he pays $5000 of tuition, he would get a $1000 credit and owe $1078 in taxes, that needs to be covered by withholding and/or estimated payments.)
The tool may also work a bit better after the second or third paycheck, since it needs to extrapolate the whole year from the income and taxes to date, and if you can give it a few more weeks of data, it may be more accurate.
