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FICA taxes apply to the full amount of the disability payment for the first six calendar months after the employee has ceased performing services for the employer. Disability payments will be exempt from FICA starting in the seventh calendar month after the employee has stopped performing services for the employer. 

The LTD insurer should have deducted those from your benefits.

https://www.irs.gov/pub/irs-wd/11-0065.pdf

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