Only compensation (wages) is subject to FICA and Medicare taxes. SEP-IRA contributions are employer contributions, not compensation. Money contributed as SEP contributions by a W-2 employer is never subject to FICA or Medicare taxes. However, SEP contributions made by a self-employed individual are a deducted after SE tax has been determined, so these contributions are made with money on which SE taxes will have been paid.
Distributions from retirement accounts are never subject to FICA and Medicare taxes.
