There are a lot of quests that are "missable" if you simply don't take the time to explore everything. As for timed quests, the burning ship quest is one of the only ones that you can fail simply by waiting too long. There are two other time-sensitive quests that I can think of right now (and one of them might only be time-sensitive because of a bug). Neither one is in Cyseal. I can't really explain them without spoiling them, but if you really want to know:

One of them is in Hiberheim and involves you helping out a rabbit. It requires that you have the Pet Pal talent. It's not a quest per se in that it doesn't have an associated journal entry, but there is content that you miss out on if you don't complete it. The good thing is that this "quest" won't actually start until you get close enough to trigger it, and when you do it's pretty obvious what must be done.

The other one is called Frederick's Blood Stone, in Luculla Forest. This is the one that's possibly bugged. Basically when you first get it, try to complete it as soon as possible otherwise something might happen that makes it impossible to finish the quest properly.