The program is correct. You are allowed up to $6,000 of expenses because you have two qualifying children. It does not matter all of the expense was for one child.
Here is an excerpt from the Instructions for Form 2441 (which is the form to claim the Child Care Credit):
To qualify for the credit, you must have one or more
qualifying persons. You should show the expenses for
each child in column (c) of line 2. However, it is possible a
qualifying child could have no expenses and a second
child could have expenses exceeding $3,000. You should
list -0- for the one child and the actual amount for the
second child. The $6,000 limit would still be used to
compute your credit unless you have already excluded or
deducted, in Part III, certain dependent care benefits paid
to you (or on your behalf) by your employer.https://www.irs.gov/pub/irs-pdf/i2441.pdf#page=3
