After you file

I think I found the problem. I dont know how this was overlooked...
When I filed the extension I entered that I paid $3,733 to the IRS already, per my W2.
When I started the process of filing a few days later through turbo tax, it did not advise me to not to enter my federal income tax withheld amount. Turbo Tax had already entered this for me when I filed the extension.
My 1040 shows my total payments to the IRS were $7,466 (double the amount I actually paid in) which is not correct.
Do I need to do an amendment ^^^
I also filed a 1099 for 2018. Before I got the letter in the mail from the IRS I realized that I did not enter all my expenses. Everything I was reading advised not do an amendment until my return was approved or rejected.
Sorry! I have lots of questions.