Note: This answer had been sent to Ali in private email (the question had been closed while I was composing it). Now that the question has been reopened, the answer may be given here. (This has been edited, but the original letter is revision 1.)
The answer to the question about $S^n$ and their hemispheres $H$ is yes, in a fairly easy way.
The inclusion $i: H \hookrightarrow S^n$ of the northern hemisphere has a retract $r: S^n \to H$ which linearly reflects points on the southern hemisphere across the equatorial hyperplane. Taking $C_1 = S^n$ and $C_0 = H$, and the domain and codomain maps $\partial_0, \partial_1: C_1 \rightrightarrows C_0$ both to be $r$, we may then define the object-to-identity map $u: C_0 \to C_1$ to be $i$, and we get a reflexive graph. Now we define composition to make this to a groupoid. the object $C_2 = C_1 \times_{C_0} C_1$ of composable pairs is just the kernel pair, i.e., the subspace of $C_1 \times C_1$ given by $\{(x, y): r(x) = r(y)\}$. Let $H'$ be the southern hemisphere and let $s: S^n \rightleftarrows H': j$ be the analogous retraction pair for the southern hemisphere, and define $m: C_2 \to C_1$ by $m(x, y) \mapsto i r(x)$ if $x = y$ and $(x, y) \mapsto j s(x)$ if $x \neq y$. It is not hard to check that this defines a continuous map.
The picture is that if you forget the topological structure and look at the underlying discrete groupoid, then there are no morphisms $a \to b$ if $a \neq b$, and the groupoid is a coproduct of groups $\bigsqcup_{a \in H} \hom(a, a)$ where $\hom(a, a)$ is the trivial group if $a$ lies on the equator, and $\hom(a, a)$ is the group $\mathbb{Z}/(2)$ if $a$ is off the equator. As a groupoid this is not connected (since there are no morphisms $a \to b$ between distinct $a, b$), although the total space $C_1$ is a connected space.