Let me make quite clear that the recent experiment does NOT imply the detection of a true magnetic monopole. Somehow, in all the excitement, the word "synthetic" was dropped rather quickly from the phrase "synthetic magnetic field".
A synthetic magnetic field is a physical quantity that obeys the same equations as a magnetic field, typically realized in things like the velocity field of the atoms inside a BEC. The recent paper claims the observation of the analogue of a Dirac monopole in such a quantity, and it is a significant result in the field of quantum simulation. However, their experiment is made completely out of atoms, and therefore of protons, neutrons and electrons. It cannot have any magnetic flux into or out of any region within or around it, and it does not violate the laws of electromagnetism. Indeed, it's built within them.
Synthetic magnetic fields are explained nicely in this review:
Colloquium: Artificial gauge potentials for neutral atoms. Jean Dalibard et al. Rev. Mod. Phys. 83 no. 4, 1523–1543 (2011). arXiv:1008.5378.
They describe a simple toy model which captures, I think the basics of the recent experiment.
Consider a two-level atom which is at the influence of an external field which couples its two internal states. Its hamiltonian can be written as
$$
H=\left(\frac{P^2}{2m}+V\right)+U,
$$
where the part in brackets does not couple to the internal state, and
$$
U=\frac{\hbar\Omega}{2}\begin{pmatrix}\cos\theta&e^{-i\phi}\sin\theta \\ e^{i\phi}\sin\theta & -\cos\theta\end{pmatrix}
$$
in the ground - excited state basis $\{|g\rangle,|e\rangle\}$. In such a scheme $\Omega$ is the Rabi frequency and determines the strength of the coupling; $\phi$ is the phase of the laser that's used to couple the states; and $\theta$ is called the mixing angle and determines whether the coupling acts more like a Stark shift (at $\theta=0$), more like a pure coupling (at $\theta=\pi/2$), or somewhere in between. The distinction between those regimes is dependent on the detuning to the atomic transition, and it can vary with the atom's position $\mathbf{r}$.
The game here is to have the atom move around slowly enough that it will always stay in the ground state of the laser-induced atomic hamiltonian $U$. This is the first of the two eigenstates
$$
|\chi_1\rangle
=\begin{pmatrix}\cos(\theta/2) \\ e^{i\phi}\sin(\theta/2)\end{pmatrix},
\quad
|\chi_2\rangle
=\begin{pmatrix}-e^{-i\phi}\sin(\theta/2)\\ \cos(\theta/2)\end{pmatrix},
$$
which depend on the position $\mathbf{r}$ through the laser parameters $\theta$ and $\phi$. If you vary these parameters slowly enough, you will stay in the same eigenstate as you started in, without any nonadiabatic transitions.
More precisely, because the states $|\chi_j\rangle$ are a basis, one can always write the atom's wavefunction as
$$
|\Psi(\mathbf{r},t)\rangle=\langle \mathbf{r}|\Psi(t)\rangle
=
\sum_j\psi_j(\mathbf{r},t)|\chi_j(\mathbf{r})\rangle.
$$
(Note that this is the position-dependent internal state, which can be obtained from the full state $|\Psi(t)\rangle$ by projecting on a position state $|\mathbf{r}\rangle$.) If the atom's velocity spread is small enough, it will never transition to $|\chi_2\rangle$ and one can describe the system simply in terms of a single Schrödinger equation for $\psi_1(\mathbf{r},t)$.
To get that equation, you first have to work rigorously with the full state, and then afterwards neglect the possibility of transitions. Thus, if you act with the momentum $\mathbf{P}=-i\hbar\nabla$ on the component $\psi_j(\mathbf{r},t) |\chi_j(\mathbf{r})\rangle$, you will get contributions from both factors:
$$
\nabla\left[\psi_j(\mathbf{r},t)|\chi_j(\mathbf{r})\rangle\right]
=\left(\nabla\psi_j(\mathbf{r},t)\right)|\chi_j(\mathbf{r})\rangle
+\psi_j(\mathbf{r},t)\nabla_\mathbf{r}|\chi_j(\mathbf{r})\rangle.
$$
Multiplying on the left with the completeness relation $\sum_i|\chi_i\rangle\langle\chi_i|$, we can obtain a nice expression for the action of the momentum:
$$
\mathbf{P}\psi_j(\mathbf{r},t)|\chi_j(\mathbf{r})\rangle
=\sum_i|\chi_i\rangle
\left[\delta_{ij}\mathbf{P}-\mathbf{A}_{ij}\right]
\psi_j(\mathbf{r},t),
$$
where $\mathbf{A}_{ij}=i\hbar\langle\chi_i|\nabla_\mathbf{r}|\chi_j\rangle$ is, broadly speaking, the rate at which nonadiabatic transitions can occur. Dotting this again with the momentum operator, one obtains
$$
P^2\psi_j(\mathbf{r},t)|\chi_j(\mathbf{r})\rangle
=\sum_{l,i}|\chi_l\rangle(\delta_{li}\mathbf{P}-\mathbf{A}_{li})
(\delta_{ij}\mathbf{P}-\mathbf{A}_{ij})\psi_j(\mathbf{r},t),
$$
as long as one can neglect a term in $\nabla\cdot\mathbf{A}_{ij}=i\hbar\nabla\cdot\langle\chi_i|\nabla_\mathbf{r}\chi_j\rangle$. This corresponds to saying that the potential's variation is only relevant to first order at the low momenta encompassed by $\Psi$.
One can then neglect the possibility of transitions, and simply ignore all the terms that have $|\chi_2\rangle$ in them. (Or one might not, in which case you can try and build non-Abelian gauge fields instead.) If you do this, all the sums go away, and you get the simple Schrödinger equation
$$
i\hbar\frac{\partial\psi_1}{\partial t}
=
\left[
\frac{1}{2m}(\mathbf{P}-\mathbf{A})^2+V+\frac{\hbar\Omega}{2}+W.
\right]\psi_1
$$
This equation is identical in form to that of a single particle under the action of the old potential $V$, an 'electrostatic potential'
$$W=\frac{\hbar^2}{2m}|\langle\chi_2|\nabla\chi_1\rangle|^2$$
which measures virtual transitions from $|\chi_1\rangle$ to $|\chi_2\rangle$ and back, and a magnetic field with vector potential
$$\mathbf{A}=i\hbar\langle\chi_1|\nabla_\mathbf{r}|\chi_1\rangle.$$
This magnetic field will be nonzero whenever $\theta$ and $\phi$ both have significant spatial dependence with non-collinear gradients.
Most importantly, this 'magnetic field' depends on experimentally controllable parameters through $\theta(\mathbf{r})$ and $\phi(\mathbf{r})$. If one can build a sufficiently clever experiment, the 'field' $\mathbf{B}$, which is really the vector field
$$\nabla\times\langle\chi_1|\nabla\chi_1\rangle,$$
can exhibit monopolar behaviour. One can create 'coupled' monopoles (i.e. separated by a finite Dirac string) or even take one of those out of the cloud to make a 'true' Dirac monopole as far as the cloud is concerned. It is my understanding that this is the case for the recent experiment. This does not, of course, imply that any net real magnetic flux is coming out of that apparatus.