Enones and hydrogenation
I read your question as asking why the C-C pi bond is reduced while the C-O pi bond is not. It appears to be possible to change the selectivity of hydrogenation based on the catalyst used (reference), but for simple palladium on carbon, reduction of alkenes (even conjugated to carbonyls) is much faster than an aldehyde or ketone. Coupled with complementary hydride reagents, which are selective for carbonyls, synthetic chemists can achieve the desired reduction without worrying about reaction of other reducible groups.