Which model are you referring to?

Hyundai's warranty replacement transmissions are rebuilt, not new.
Apparently the rebuilding work is contracted out to a third party whose
chief incentive is to quickly crank quantitities of transmissions out
rather than to produce quality work.

When the automatic transmission on our 2000 Sonata went bad, the dealer
had to replace it 3 times before we received an acceptable unit. No
idea how long it will last, but needless to say we don't have a real
warm and fuzzy feeling about it.

While Hyundai has made great strides in in the last several years it
seems that if you do suffer a major failure you're getting into a
revolving-door situation of trying out rebuilt parts of uneven quality
until you get one that works.