After you file

You had 488 refund online 35a.   That includes credit for the other half 3,000 on line 28.   You got it.  It reduced your total tax by $3,000 so you only get 488 now.  The 3,000 doesn't come separately it reduced your tax due.  It was already accounted for.   If you didn't get credit for the $3,000 then you would have had a $2,512 tax due (488-3,000).  Follow the math from line 24 - 35.

 

I found this in a news article, it explains it pretty well........

While the CTC expansion was structured to not increase taxes on any household, a dollar of credit received in advance results in a dollar less received at filing time. For families unaware of the trade-off, it could mean a surprise when they see their refund total this year.

 

Consider a married couple with a 10-year-old child who normally received their $2,000 CTC when they filed their taxes. They would have received $1,500 of their $3,000 in advance. As such, they could potentially see their refund shrink by $500 even though their total benefit increased to $3,000 because they are left with $1,500 instead of their normal $2,000 at tax time.