After you file

I filed my return electronically through TT.  In July I received a notice from the IRS regarding changes to my return increasing tax due.  When I went back into TT I was presented with a new return showing increased tax equal to the IRS calculation; obviously adjustments were made to my return that matched the IRS adjustments.  In essence, TT was telling me that I owed additional tax to the IRS exactly equal to my IRS notice.  How can this be??

 

My question then is how did these changes get added to my TT file/return?  And, if the program is making changes shouldn't I be notified?

Peter