Is this the first year they have done that?  What happened in 2018?

On the rejected return, what amount do you have on Line 21?  It should be $2,500.

The 2441 instructions seem to contemplate a situation where an MFS filing can claim the exclusion in Part III.  There is probably a convoluted path to an answer, if you want to spend half a day researching it. 

Line 19
If your filing status is married filing separately, see Married
Persons Filing Separately, earlier. Are you considered
unmarried under that rule?
Yes. Enter your earned income (from line 18) on
line 19. On line 21, enter $5,000.
No. Enter your spouse's earned income on line 19. If
you or your spouse was a full-time student or
disabled in 2019, see the instructions for lines 4 and
5. On line 21, enter $2,500.