Retirement tax questions

So I did a little more digging... Here's what happened in 2018.  I contributed the full 5500, but only took out 2500 before April 15 2019 deadline.  This is what TurboTax advised me to do, based on my income....  What frustrates me is that this advice was incorrect, relooking at my gross income, I had made just barely more than 135000 and I should've been advised to take ALL of the 5500 out.  So I'm going to be penalized for taking turbo tax's advice of only removing 2500.  But the excess number of 3000 in my 2018 return form 5329 is probably correct, and doesn't need amending?