If you and your husband lived together- Yes, the $2500 will be taxed. As long as you properly enter your W2 with Box 10 of $5000, and you visit the Dependent Care Credit section of Turbo Tax- the program will carry the $2500 into your 1040.
If you didn't live with your husband for the last 6 months of 2016, and are eligible to file as Head of Household, then your FSA limit will remain $5000.
This is also assuming that you are claiming the child if filing Married Filing Separately. If your husband is claiming the child, you will need to repay the entire $5000.
