We can't see what your employer's system does with the W-4, and we have no way of knowing whether it's doing it correctly.
Step 3 on the IRS W-4 form basically adds up any credits that you might be entitled to claim on your tax return. It gives you specific instructions to calculate the child tax credit and credit for other dependents, and tells you to add other credits. The question about your income being less than $200,000 relates to the child tax credit. If you have no dependents you will not get the child tax credit or the credit for other dependents. So it makes no difference whether you answer No, or answer Yes and enter zero dependents. Either way the credit is going to be zero.
If your employer's system is doing the calculations correctly, there's no reason for you to change it or submit another W-4. Even though your answer was technically incorrect, the result should be the same as if you had answered correctly. If you can see the actual W-4 form that they fill out, you can check to make sure that line 3 is zero or blank.
