Line 2 on the 8889 has any money you contributed to your HSA with after-tax dollars, no pre-tax dollars.
Line 9 has the total of what your employer and you through payroll deduction contribution to your HSA (generally this is the amount with Code W in box 12 on your W-2).
"The difference is what my employer gave as "free money" to my HSA but only to a limit based on matching our contribution. " I don't understand what you mean by this. Are you saying that the employer gave you after-tax dollars to put in your HSA? If so, that would go on line 2, but this is an unusual arrangement. This means that this "free money" was included in Wages in Boxes 1, 3, and 5 on your W-2 and is not in the code W amount in box 12.
"employer matching is not suppose to be in that amount."
If the employer matching is included in the code W amount and is NOT removed from Wages in boxes 1, 3, and 5, this this would be true...but this is really unusual.
Unfortunately, you can't tell from looking at the W-2 if the "free money" was included in your wages - you have to ask your HR department to be sure.
If the "free money" is NOT in your wages on the W-2, then it should have been included in the code W amount. In this case, you would have to ask for a corrected W-2.
Note that code W amount often does not match the 5498-SA because of excess contributions returned, contributions made in subsequent years, and so on.
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