Just obtained these two crates of wine and have no idea what to do with them. I've read that im supposed to give it Ludwig the innkeeper, but again, no option appears to do so.

Any ideas?

Yes, Chateau de Trebrechette is meant for the innkeeper Ludwig Weintraum from West Glatzburg. You will accept his quest "Bring Chateau de Trebrechette" during the very first dialogue with him. If you have the wine on you during the first dialogue already, the quest will be completed at the same moment it will be accepted. It seems to me that there is no way how to not obtain the quest and I believe this quest should work properly.

But as you have mentioned, you can find two crates of the wine, in fact. The innkeeper will take only one crate though which means that you can do whatever you want with the second one.

I think i may of rejected that quest. Is there anyway to give it to him? or sell it?

Well... it seems you are right and there is an option to reject that quest. In that case, there is no way to give the wine to him and since the wine is a quest item, you cannot sell it. But you can destroy it.