Roth IRA Distribution code wrong

I have a Roth IRA that I started at Company A roughly 15 years ago, deposited a few thousand to start. I then rolled it over to Company B continued to add money yearly. 7 years ago I rolled it over to Company C and continued to deposit money. 

This year I had a large purchase (Rooftop Solar) which I withdrew most of what I contributed  over the years. ALL of the gains were left untouched plus some what I contributed over the years. 

I received a 1099-R from Company C for the withdraw and the Distribution code was "J" for early withdraw. I called them and said they made a mistake but they said they show a withdraw in excess of what I deposited while the account was with them. They couldn't account for the other 2 companies. 

I'm confidant I could show my records of deposits via previous tax returns but I don't know what to do to correct the 1099-R distribution code. I use the code that company C gave me the software marks it as an early withdraw and charge me with a large early withdraw penalty. But I don't want to change the code manually because the form states otherwise.