Since she is Married Filing Separately, she is not eligible to claim or receive the Premium Tax Credits for health insurance through the Marketplace unless she is a victim of abuse or spousal abandonment.
If she did receive the credit, then he or she will need to repay the credit depending on how they work it out. This will be added to whichever persons tax liability and become part of the taxes due or result in a decrease in their refund.
If both of them are on the 1095-A, they will need to select that they shared the policy with another taxpayer and both of them will need to enter the form on their returns. They will then need to agree on an allocation amount from 0% to 100%. It does not matter who paid what, it can be allocated however they agree to allocate it.
If she had her own 1095-A, then she will just need to enter it on her return.
If they paid the full premium and did not get any credit, then there will be no affect on her return.
Depending on their situation, even if they are separated, they may be better off filing a joint return.
Premium Tax Credit MFS
Form 8962 Instructions
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