When all else fails Read the Instructions: https://www.tax.ny.gov/pdf/current_forms/it/it201i.pdf

Line 29 – Pension and annuity income exclusion
Did you enter an amount on line 9 or 10 that was not from a NYS or local government pension plan or federal government pension plan? If No, go to line 30.
If Yes, and you were 59½ before January 1, 2019, enter the qualifying pension and annuity income included in your 2019 federal AGI, but not more than $20,000. If you became 59½ during 2019, enter only the amount received after you became 59½, but not more than $20,000. If you received pension and annuity income and are married, or received pension and annuity income as a beneficiary, see below.
$20,000 limit – You may not take a pension and annuity income exclusion that exceeds $20,000, regardless of the source(s) of the income.

And if you keep reading the instructions it specifically states that if you’re MFJ then EACH taxpayer is entitled to a $20k exclusion. Hence my original question. This has been existence for NYS purposes for years.

I stand corrected. Highlight the client and use Ctrl + L to open a ticket with Lacerte to report the program error. You can attach the client file to show how the input was done, so they can confirm the flaw and correct it. 

Yes I already put in a question to Lacerte as well. Waiting to hear back from them

Did anyone get a resolution for this yet?  Still only one pension exclusion flowing through

i sent an email to tech support on Saturday about this, waiting to hear from them. I just did another update, but that didn't fix the issue. At least it's not just me that's having this issue!

i called lacerte about this yesterday, it's being worked on, no resolution at this time. It's now holding up a number of returns for me!

I too am having this issue, Sunday February 16.