They dont contradict eachother. Bestiary says you need certain kinds of material to bypass them. Core book says certain enhancements count as a certain kind of material for the purpose of overcoming damage reduction. Both are correct.
Its the same as saying a half elf counts as an elf, and then another book saying you must be an elf to take x feat. The half elf can take that feat.
Kolokotroni is correct. I don't have my book with me, so I can't find the page, but it states that the enhancement bonuses (+1,+2, etc..) are strong enough to bypass certain damage reductions. This also includes weapons like a +1 Flaming Longsword counting as a +2 weapon.