Bugs, meaning my saves are broken? Or its just the current state of co-op?
I had the same problems in the alpha/beta. Basically if you went too far away from the other character/waited too long/ initiated dialogue with another npc. Before you talked to your partner then you would lose out on some dialogue.
What I mean is that there are still plenty of bugs in the game. And Larian will probably patch them. So I reckon (like with all games on release) that you either have to wait a bit if you don't want to miss out on anything dialogue/quest wise. Or just have to live with the missed dialogue for now. It is bound to happen that you miss some of them sadly.
Edit: Think i misunderstood you. If one player initiates dialogue with an npc, then you don't both get the dialogue tree unless they are special npcs. If that was your issue then yes that's the way it is sadly. Which means you both have to talk to npcs if you both want to get everything. It should show up as floating text over the character speaking however. BUt it is way less convenient than say old crpg games like baldur's gate, where both would see the dialogue on one screen.
I suggest doing what we do, read the text out loud on skype/vent etc. However that can be very tiresome as it is a text heavy game.