Normally, unexpected results on the HSA (like distributions being taxed) occur because the taxpayer h
as not yet completed the HSA interview. There are HSA questions even beyond the "
Your HSA Summary" screen that would appear to signal the end of the interview.
Contributions to an HSA are normally excluded from income. Distributions made for qualified medical expenses are not taxable. So if either appears to be taxable, go back to the HSA interview (Federal Taxes->Deductions & Credits->Medical->HSA, MSA, Contributions), and run all the way through it, checking the answers.
Since the HSA operates in a way similar to an IRA, it is common for distributions to be more or less than contributions; any unspent amount simply carries over to next year.
As for the possible confusion of your contributions versus employer contributions, note the following:
It is counter-intuitive but employee contributions to an HSA made
through a salary reduction plan with the employer are called employer
contributions by the IRS. This is because both the contributions made by
the employer and contributions made by the taxpayer through a salary reduction
arrangement are treated the same way (they are both pre-tax).
The IRS says in Publication
969: "Contributions made by your employer aren’t included in your
income. Contributions to an employee's account by an employer using the
amount of an employee's salary reduction through a cafeteria plan are treated
as employer contributions."
