I think what you are saying is that your employer withheld too much for your taxes because they incorrectly calculated your taxable income, with the result that you paid too much in taxes because your taxable income would have been lower if your employer had correctly deducted the employee-paid portion of your insurance premium from your earned income, and had correctly reported your gross taxable wages.
If that is not correct, please let me know. This answer assumes the above is correct.
For the current year, you need to demonstrate to the IRS that some of your employee-paid premiums were included in Box 1 of your W-2, which under normal circumstances they should not be. In that case, they would be deductible as described by the IRS here. The language you quoted assumes that the premium has already been correctly deducted from your taxable income as reported on your W-2.
Please note that the portion of your premium that was paid by your employer, as well as the portion of your premium that is employee-paid that was correctly deducted from your earned income cannot be deducted on your taxes, as they have already been treated as pre-tax. In order to be able to deduct medical expenses via the 10% rule, you have to have incurred additional expenses beyond what has already been treated as pre-tax. So you would need to have incurred 10% worth of additional expenses in order to claim the deduction, including the amount incorrectly not deducted from your earned income, but excluding the employer and employee-paid portions of the premium that were correctly deducted (these amounts would not count toward the 10% as documented in the linked article). You need to verify that the expenses not already considered pre-tax are over 10% (including any amount correctly deducted), not just that the total employee-paid portion of the premium is over 10%.
However, for the previous tax years where you have possibly already overpaid on your taxes due to the error, you now have a legal issue with your employer.
You will have to decide whether the potential tax savings for this year and the potential restitution for previous years are worth a potential audit for the current tax year (which is its own headache and expense), and/or finding a new job and/or the time and expense of a lawsuit if things go badly with your employer. If you do decide to pursue action on your own, be sure to prepare seriously and consult a lawyer and/or a CPA before making any allegations against your employer. If they broke the law, both the company as well as the individuals involved could be penalized.
Lastly, I'd strongly recommend considering whether you want to continue to work long-term for a boss whose answer wasn't "We'll find out what went wrong, and make it right".