IRA excess contribtution

TP made $28000 contribution from regular investment account to her traditional IRA account by error. She discovered the error and noticed Charles Schwab, the IRA custodian. TP received 5498 form showing $3000 in box 1 and $25000 in box 2 .
My questions are:
1. How are the $3000 in box 1 and $25000 in box 2 calculated?
2. The correction was made before TP filed her tax return but she did not inform me of the excess contribution and correction.
So, now I need to amend TP's return to include the NIA (net income attributable) in her income and also the 10% early withdrawal penalty on the NIA, right?
to clarify, the correct amount of withdrawal should be excess contribution plus NIA, right?
3. also, will there be any impact on her 2021 tax?

Thank you!

When was the $28k contributed? During 2020 or in 2021 before the original due date of the return?

in 2021 before the original due date of the return

Then the allocable earnings with penalty are reported on the 2021 return. 2020 does not need to be amended.

Then the allocable earnings with penalty are reported on the 2021 return. 2020 does not need to be amended.

sorry, I read your question wrong. I thought you asked for correction time.
TP made excess contribution in April 2020 and made correction in March 2021.

The reporting follows when the contributions were made.

If the $28k was contributed during 2020, the allocable earnings and 10% penalty goes on the 2020 return. i.e. amend

Next year you'll get a 1099-R that you can ignore. (should have the "prior year" code on it)

Thank you!