Here's one cute example: consider the Boolean algebras $\mathcal{B}:=\mathcal{P}(\omega)$ and $\mathcal{A}:=\mathcal{P}(\omega)/\mathit{fin}$, where $\mathit{fin}$ is the $\mathcal{B}$-ideal of finite sets. Clearly $\vert\mathcal{A}\vert\le\vert\mathcal{B}\vert$ (at least, assuming choice :P).
However, it turns out that there is no embedding from $\mathcal{A}$ into $\mathcal{B}$ for a simple structural reason: even though $\mathcal{A}$ is a quotient of $\mathcal{B}$, $\mathcal{A}$ is "wider" than $\mathcal{B}$!
Wait, what?
Let the width of a Boolean algebra $\mathcal{X}$ be the supremum of the cardinalities of sets $U\subseteq\mathcal{X}$ such that for all $u,v\in U$ we have $u\wedge v=0$. (Incidentally this is not standard terminology - I don't know if there is a standard term for this.)
In $\mathcal{B}$, the equation "$u\wedge v=0$" just means that $u$ and $v$ are disjoint. Consequently we obviously have $\mathit{width}(\mathcal{B})=\aleph_0$. It's also easy to see that if $\mathcal{X}$ embeds into $\mathcal{Y}$ then $\mathit{width}(\mathcal{X})\le\mathit{width}(\mathcal{Y})$.
However, it turns out that $\mathit{width}(\mathcal{A})=2^{\aleph_0}$. This is quite surprising at first (at least it was for me), and amounts to the following combinatorial result:
There is a size-continuum set $\mathcal{F}$ of sets of natural numbers which are pairwise almost disjoint, that is, such that for $u,v\in\mathcal{F}$ we have $u=v$ or $u\cap v$ is finite.
This is a fun puzzle, so I'll hide a hint below:
Think about Dedekind cuts.
Complete solutions have appeared in various places across this site (search for "almost disjoint family" or similar); here is one of mine, where I break the problem into separate (hidden) hints.
Finally, note that if $\mathcal{X}$ is a quotient of $\mathcal{Y}$ then every antichain in $\mathcal{X}$ "comes from" an antichain in $\mathcal{Y}$. The definition of width may look odd at first, but it's exactly this stronger requirement "$u\wedge v=0$" that allows it to play interestingly with quotients: if we just looked at the supremum of the cardinalities of the antichains, things would be pretty boring.