Federal taxes are withheld based upon the W-4 form that you gave your employer.
Assuming you mean "for" Social Security taxes, the answer is that it is typical for lower income employees to pay more Social Security and Medicare taxes than Federal Income tax. As income increases, the balance shifts the otehr way because the Federal Income tax percentage rates increase as income rises but Social Security and Medicare tax rates stay the same except for very high income taxpayers.
What is the income threshold for this? For example let's say i make 45k a year and my spouse makes 39k but have withheld almost 500 more in ss taxes than federal, as for myself I pay almost double in federal than ss taxes. Is 6k a year that big of a difference?
Social Security tax is calculated by multiplying the gross income for a pay period by 6.2%. The difference likely comes from how your W-4 was filled out to withhold tax. If you didn't claim any dependents or chose married filing separately vs. married filing joint more taxes would be withheld for federal taxes, resulting in your federal taxes being withheld to be higher. The more dependents claimed or a married filing joint claim on the W-4 results in less federal taxes being withheld.