Well...historically, (at least in recent history) , werewolves are traditionally at conflict with vampires, so I don't see why they couldn't be in conflict in Dawnguard..
If by "recent history" and "traditionally" you mean "since Underworld". Traditionally vampires were werewolves, in the old tales. But vampires and werewolves today are nothing like how they used to be anyway, so whatever. They're still not like Underworld.
(I mean, both pieces are there, why not put them into play?)
Because the critical piece is missing: motivation. Just because you have werewolves and vampires doesn't mean they have to hate and be at war with each other. There is no reason for them to hate each other, and making up a reason would just come off as a lame excuse. Especially when you consider that people in the Elder Scrolls are individuals, and aren't defined by the race or group they belong. Vampires have individual aspirations and are people first, but with a twist of having a dark underside to them. It's not "I'm a vampire, so I must hate werewolves" or "I'm a werewolf so I hate vampires" like in other media.
If a vampire hates a werewolf it's because that particular vampire has a personal reason to, not because of some divine mandate that says he must because he's a vampire.