By "tax preparer", I presume you mean the person e.g. bookkeeper, who completed your tax return.
When you phone the tax office, be sure to have all your dates, salary slips, reference numbers, etc., together. Start by saying that you're not sure that you understand what they've sent you, and then they'll probably connect you to the right person who can explain it.
Once you reach that person, say that you don't understand the bill you've received from them, and that you want to be sure to do the right thing tell them what kind of permit you have add that you think your bookkeeper, who submitted your tax return, might have omitted to include your Lohnausweis for that year, and ask whether they do/don't have it ask them to please check whether or not your former employer properly paid in the taxes they had deducted from you also, if you were here during the year prior to the one with the mix-up, ask them to check whether that previous year is all properly paid up ask them whether any payments have been made by your employer, for the following year. They might be willing to send you print-outs of each year.
Points 4. to 6. are because of what nopeno wrote, above, that it could be that payment was made, but landed in the account of a different calendar year. Been there, done that.
Then ask them what the correct steps are, from here on.
If, in fact, your former employer really did deduct taxes from your salary but neglect to pay those in, chase up the employer. Also: check with the AHV (mandatory social security) whether that employer also neglected to pay in your compulsory contributions, there, too. You don't want to have gaps.