There are two ways for an HSA owner to correct an excess contribution – by removal or by applying it in a subsequent year. You must withdraw the excess contributions and any earnings to avoid the 6% penalty tax.
Removal: To correct an excess HSA contribution and avoid a 6 percent penalty tax, an HSA owner must remove the excess amount from the account by the deadline (04/18/2017 unless you file an extension). The net income attributable to the excess amount must accompany the distribution of the excess. Because a tax deduction is not allowed for an excess contribution, when removed it is not taxable. However, any net income attributable to an excess is subject to tax in the year of the distribution.
Applying in a subsequent year: An HSA owner could apply the entire excess amount to a subsequent year, assuming the regular contribution, including the applied amount, does not exceed the limit for that year. However, he/she would owe a 6 percent penalty tax for each year he/she fails to correct the excess.
IRS
Pub 969
