They are not reporting 9,000 shares, they are reporting two payments against 4,500 shares. Simply report one sale of 4,500 shares with proceeds of amount1 plus amount 2.
"Also we did not file any AMT in any previous tax year. Would this impact the 2016 tax calculation ?"
I don't know if you'd have been subject to AMT in 2014, 2015 and now 2016, but if you are saying that you didn't report the "spread" between exercise and FMV in 2014, 2015 and now 2016 as an AMT adjustment item, that's not correct. You might want to go back to those 2014 and 2015 income tax returns and see if you should have been subject to AMT. If you're not, then there's no problem. If you should have been you probably should amend those two years. The 3,500 shares you acquired as part of the acquisition would also, I'm pretty sure, be considered an "exercise" that also needs to be reported for AMT purposes.
You might be better off dealing with a local professional here.
