Here's an example of an incomplete but transitive preference.
Consider three fruits, an apple ($A$), a banana ($B$), and a coconut ($C$). I cannot choose between individual fruits, i.e. I don't have a preference over $A$, $B$, or $C$ --- not that I'm indifferent between them, I just can't compare them. However, I do prefer more variety to less, namely, I'd choose a bundle with two fruits, e.g. $\{A,B\}$ over a bundle with only one fruit, say $\{C\}$.
It's easy to see that my preference over bundles of fruits (the powerset of $\{A,B,C\}$) is incomplete, since it is not defined over singletons. However, my preference is still transitive, in that whenever bundle $X$ is preferred to $Y$ and $Y$ preferred to $Z$, $X$ is preferred to $Z$, for example, $\{A,B,C\}\succ\{B,C\}\succ\{C\}\;\Rightarrow\;\{A,B,C\}\succ\{C\}$.