If my husband is incarcerated is he still penalized for not having health coverage?

[DoninGA]

No.  If you go through the Health Insurance section of the program and are filing as Married Filing Jointly you would choose the option I'll pick who had it and which months.  For your spouse you would only check any months that they had insurance.  On the following screen select Spent time in jail as the exception.  Continue with this section until it completes.