Question:
Does there exist a Riemannian manifold, with a point $p \in M$, and infinitely many points $q \in M$ such that there is more than one minimizing geodesic from $p$ to $q$?
Edit:
As demonstrated in Jack Lee's answer, one can construct many exmaples in the following way:
Take $X$ to be a manifold which has a pair of points $p,q$, with more than one minimizing geodesic connecting them. Take $Y$ to be any geodesically convex (Riemannian) manifold. Then $X \times Y$ satisfies the requirement:
Indeed, let $\alpha,\beta$ be two different geodesics in $X$ from $p$ to $q$.
Fix $y_0 \in Y$, and let $y \in Y$ be arbitrary. Let $\gamma_y$ be a minimizing geodesic in $Y$ from $y_0$ to $y$. Then $\alpha \times \gamma_Y,\beta \times \gamma_Y$ are minimizing from $(p,y_0)$ to $(q,y)$.
Hence, if $Y$ is positive-dimensional (hence infinite), we are done.
"Open" question: Are there examples which are not products? (This is probably hard, I am not even sure what obstructions exist for a manifold to be a topological product of manifolds)
Note that for any $p$, the set $$\{q \in M \,| \, \text{there is more than one minimizing geodesic from $p$ to $q$} \}$$
is of measure zero.
Indeed, let $M$ be a connected Riemannian manifold, and let $p \in M$.
The distance function from $p$, $d_p$ is $1$-Lipschitz, hence (by Rademacher's theorem) differentiable almost everywhere.
It is easy to see that if there are (at least) two different length minimizing geodesics from $p$ to $q$, then $d_p$ is not differentiable at $q$. (We have two "natural candidates" for the gradients).