On the one hand, one might expect that there can be no fully satisfactory example of the phenomenon, in light of the observations mentioned in the comments, namely, that every partial order fulfilling the Zorn's lemma hypothesis can be extended to one in which also every chain has a least upper bound. In effect, one adds nodes to play the roles of those least upper bounds.
The point is that instance of the phenomenon that someone might present can immediately be criticized as unnatural on the grounds that it is incomplete — by forming the completion, we could have chosen an equivalent but better version of the poset, one achieving exactly the same maximal elements, but in which every chain has a least upper bound.
In this sense, the question is fundamentally concerned with whether there are natural partial orders in which every chain is bounded but for which the least upper bound property fails. Indeed there are, and I shall mention several.
Let me begin by observing that every application of Zorn is equivalently made with an order not having the LUB property.
Duplication orders. Take any partial $\mathbb{P}$ and consider the duplication order $\mathbb{P}^*$, in which every element has been duplicated, replaced with two or more clones that are incomparable to each other but ordered with respect to the other elements according to the original order. Every chain in $\mathbb{P}^*$ has an upper bound, if this was true for $\mathbb{P}$, but now there are no least upper bounds for chains not having a largest element, since any of the clones works equally well. The duplication construction is often used for various purposes in mathematics, and this example shows furthermore that every application of Zorn's lemma can be turned into an example of the requested incomplete phenomenon.
But let me also mention several other examples of naturally occuring partial orders in which every chain has an upper bound, but many chains do not have least upper bounds.
Hausdorff order. The Hausdorff order of almost inclusion on subsets of $\mathbb{N}$ is a natural order where every chain has an upper bound, but many chains do not have least upper bounds.
Namely, the almost-inclusion relation $A\subseteq^*B$ for subsets $A,B\subseteq\mathbb{N}$ holds when all but finitely many elements of $A$ are in $B$. One can take equivalence classes with respect to the almost equal relation $A=^*B$, and induce the order on the quotient.
Every chain has an upper bound in its union, but nontrivial countable chains never have least upper bounds, as Hausdorff proved. So this is a natural order where every chain has an upper bound, but many chains do not have least upper bounds.
Turing degrees and the exact pair phenomenon. Another type of partial example occurs with the Turing degrees. Every countable chain in the Turing degrees has an upper bound, simply by encoding the whole chain, but no nontrivial countable chain has a least upper bound in light of the exact pair phenomenon, by which every increasing countable chain admits (diverse, nonunique) pairs above, such that any point below both is below something in the chain.
If one were simply to add a node atop the whole structure, then every chain would have an upper bound, but no nontrivial countable chains would have least upper bounds, providing another example. But see this related question, Does every countable set of Turing degrees have an upper bound, without AC? So the Turing degrees are an interesting case in the absence of AC.
Mod(T). Consider the class of models of $T$, a first-order theory. This is naturally ordered by the submodel relation, but the property that unions of chains of models of $T$ is still a model of $T$ is equivalent to having an $\forall\exists$ axiomatization. Such kinds of theories are quite common, because with $\forall\exists$ assertions the theory can express certain basic closure properties. But some theories $T$ do not admit such an axiomatization, and in this case, the union of a chain of models of $T$ will not generally be a model of $T$, but by compactness there will always be upper bounds. For example, if $T$ is the theory of a dense linear order with a largest element, then every chain is contained in a model of $T$, but we will often have a choice in placing a new largest element.
Surreals. The class of surreal numbers have the property that every set of surreals is bounded, but no set of surreal numbers has a least upper bound or greatest lower bound, except by containing a largest or least element already. The reason is that for any set $A\subset\text{No}$ with no largest element and any upper bound $A<b$, there will be smaller upper bounds $A<c<b$ added at the next available stage after all the elements of $A$ and $b$.
Conway games. More generally, the Conway games generally provide a nonlinear order with the same property. The Conway games admit a natural order (see this article), and while every set of games is bounded, chains do not generally have least upper bounds.
The last few examples are proper class examples, and they only exhibit the every-chain-is-bounded property for set-sized chains. That feature is not sufficient to produce maximal elements via Zorn — for example, every set of ordinals is bounded, but there is no largest ordinal. Nor are there maximal surreal numbers nor maximal Conway games.