Roth gains are taxable if you make a withdrawal prior to retirement age. Contributions can always been withdrawn tax free, since they are post-tax contributions to begin with.

OP, they should've only refunded your contributions, not any gains at all. I believe the form you need is 8606. It allows you to enter your cost basis (your contributions) and your withdrawal amount. Since your withdrawal will be less than your cost basis, you'll owe $0 taxes on that $ once you complete the correct form. Your tax program will have the form, but you'll likely have to search for it, it probably will not prompt you to fill it out on it's own.