Given a simplicial complex $X$, and a family of its subcomplexes $\{U_i\}_{i\in I}$, we define the corresponding intersection complex to be the simplicial complex $X_U$ with vertex set $I$ where $A \subseteq I$ form a cell whenever $\bigcap_{i\in A} U_i \neq \emptyset$. If in addition $\{U_i\}_{i\in I}$ covers $X$, i.e. if $\bigcup_{i\in I} = X$, and each $U_i$ is connected, we call $X_U$ a cover complex of $X$.
The question is:
If $X$ is a (finite) simply connected simplicial complex, must each cover complex of $X$ also be simply connected?
Here is an incomplete proof sketch. The case where $X$ is homeomorphic to the unit disc in the plane is easier (proof?). Let $C= v_0 v_1 \ldots v_k=v_0$ be a cycle in the 1-skeleton of $X_U$. We can restrict our attention to the case where $C$ is induced, i.e. no edge of $X_U$ connects vertices at distance at least two along $C$, because those cycles generate $\pi_1(X_U)$. Notice that such a cycle gives rise to a cycle $C’$ in $X$, obtained by uniting paths between $v_{i-1} \cap v_{i}$ and $v_i \cap v_{1+1}$ for each $i$. Since $X$ is simply connected, there exists a continuous map $F: D^2 \to X$ such that $F$ restricted to $\mathbb{S}^1$ traverses $C’$. If $F$ is bijective, we can reduce to the case where $X$ is homeomorphic to the unit disc mentioned above. If not, I hope that the disc case can be generalised…
Example: The answer is positive when $X$ is a tree. In this case $X_U$ must be a flag complex, i.e. every $k$ clique of the 1-skeleton $G_U$ of $X_U$ spans a $k$-cell. Moreover, it is known that $G_U$ is a chordal graph, which implies that the triangles of $G_U$ generate $\pi(G_U)$. Since $X_U$ is flag, each triangle of $G_U$ spans a homeomorph of a disc, and it easily follows that $X_U$ is simply connected.
Remarks on notation: The term intersection complex is standard, but cover complex is made up. Has it been studied under a different name?
If we replace cover complex by intersection complex in the question the answer is easily no, as we can remove vertices to create holes.