Retirement tax questions

I seems you did your own calculation of the allocable earnings, then took it all out yourself.

In which case, the custodian's 1099-R is correct.

 

you can't resolve an "excess plus earnings" without the custodian's help  unless you make up a  replacement 1099-R showing the excess plus earnings

Report the distribution and allocable earnings on your 2024 tax return.

 

Any red flags are of your own doing. There's no provision for an explanation at tax filing.