See this is exactly why I say that I have given up and just accept that it's math that I am not supposed to understand. You guys are coming up with numbers way different than what you claim they should be. That's what I have seen all my life in the few times I have ever sat down and tried to get my head around this stuff.The Social Security tax rate is 6.2% (for the employee). If your total compensation subject to SS tax was $99,102.54 then your SS tax should have been $6,144.36 (though it might be a bit different due to accumulated error from multiple payments). The $7,020.96 shown on your W-2 is consistent with $113,241.29 in SS wages. What does Box 3 of your W-2 show? If it shows $99,102.54, then your employer withheld $876.60 too much and you are entitled to that money back. First work with the employer to get a corrected W-2 and payment of the excess. If they won't work with you, then file IRS F0rm 843.
The Medicare tax rate is 1.45% (for the employee). If your total compensation subject to Medicare tax was $99,102.54 then your Medicare tax should have been $1,436.99. The $1,686.06 shown on your W-2 is consistent with $116,280.00 in Medicare wages. What does Box 5 of your W-2 show? If it shows $99,102.54, then your employer withheld $249.07 too much and you are entitled to that money back. First work with the employer to get a corrected W-2 and payment of the excess. If they won't work with you, then again use Form 843.
If you are okay with paying an extra $1,125.67, then that's your choice.
You want to know the numbers behind applied physics, electrical whatnots and mechanical whatevers? No problem! I can give you those to whatever decimal place you want day in and day out.
Ask me what my tax numbers are and why they don't add up and I have no answers other than I am sure they never have added up which is why I base my work Vs time value on what I take home not what they or anyone else says. To me it's math that does not add up and the people who have the power to do anything about it clearly have zero interest in letting me know what's what behind the numbers so I can see what they are figuring.
As for getting screwed by my employer well it's entirely possible. Around here it's rare to not hear about one if once more companies getting hauled into court and loosing for cheating their employees on their owed pay Vs the contract work they took on. Especially government funded and large corporate jobs where employee pay was well defined.