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the problem is that blood can be check only so thoroughly - some illnesses only develop much later and can only be tested for then, especially on a large scale. That's why in most countries the first donation is not actually used for anything besides testing.
Anyway, plasmapheresis/apheresis has the risk of a reaction to the sodium citrate that is used as a anticoagulant - there are systems that use no sodium citrate but they increase the risk for embolisms. Sodium citrate can cause hypocalcaemia, seizures,hypertention and a few more things,but generally it's safe in the donor setting.