Let $G$ be a group with normal subgroup $N \triangleleft G$. Let $\pi: G \to G/N$ be the quotient map.
Is the induced map on the group cohomology with coefficients in $U(1)$, i.e., $\pi^*: H^n(G/N,U(1)) \to H^n(G,U(1))$, injective?
(If this is not true in general, is it perhaps true for finite groups or Lie groups?)
It's definitely not true, even for finite groups. In all that follows, all coefficients will be trivial $G$-modules, and $G$ will be finite.
Firsr of all, note that as groups, $S^1\simeq \mathbb{Q/Z}\oplus V$ where $V$ is some $\mathbb{Q}$-vector space. In particular, since $G$ is a finite group, $H^*(G,V)=0$ for $*>0$, so $H^*(G,S^1)\simeq H^*(G,\mathbb{Q/Z})$ for $*>0$.
Then we have a short exact sequence $0\to \mathbb{Z\to Q\to Q/Z}\to 0$ and $H^*(G,\mathbb Q)=0$ for $*>0$ so that $H^*(G,\mathbb{Q/Z}) \simeq H^{*+1}(G,\mathbb Z)$ for $*>0$, all of this being natural in (the finite ) $G$.
So your question becomes (for finite groups) : is $H^*(G/N, \mathbb Z)\to H^*(G,\mathbb Z)$ injective for $*>1$ (knowing that for $*=0$ it trivially is, and for $*=1$ both are $0$ so it is injective too) ? The answer to that is well-known to be no. As per the comments, here's an example :
Consider $G= C_4\times C_2$ ($C_n$ the cyclic group of order $n$) and $G/N = C_2\times C_2$. Then we know that $H^2(C_2,\mathbb Z)\to H^2(C_4,\mathbb Z)$ is multiplication by $2$ from $C_2\to C_4$ and so $H^2(C_2,\mathbb Z)\otimes H^2(C_2,\mathbb Z)\to H^2(C_4,\mathbb Z)\otimes H^2(C_2,\mathbb Z)$ sends $1= 1\otimes 1$ to $2\otimes 1 = 1\otimes 2 = 0$ and in particular isn't injective. By the Künneth formula, it follows that $H^4(C_2\times C_2,\mathbb Z)\to H^4(C_4\times C_2,\mathbb Z)$ is not injective.