What follows is a partial answer with a reasonable prospect of being polished into a fuller one.
A family of subsets $\mathcal{F}$ of the finite set $[1,\ldots,n]$ is a distinguishing family iff for any two distinct $A,B \subseteq [1,\ldots,n]$, there exists $X \in \mathcal{F}$ such that:
$$ |A\cap X| \neq |B\cap X| $$
The claim is there exists a distinguishing family $\mathcal{F}$ satisfying:
$$ |\mathcal{F}| \leq \frac{(2 + o(1)) n}{\log_3 n} $$
Letting $|\mathcal{F}| = m$, an equivalent statement is:
$$ \frac{n}{m \log_2 n} \geq \frac{1}{2} \log_3 2 - o(1) $$
with $\frac{1}{2} \log_3 2 \approx 0.31546$.
We are able to show the existence of infinitely many $n$ for which this can be met.
The problem of finding a small(est) distinguishing family $\mathcal{F}$ can be restated in terms of a binary (zero/one) $m\times n$ matrix $M$ such that multiplication by $M$ is an injective (one-to-one) map from $\{0,1\}^n$ into $\mathbb{N}^m$. Here the $m$ rows of $M$ are binary representations of the $m$ sets $X_i$ belonging to $\mathcal{F}$.
If $M_{ij} = 1$ when $j \in X_i$ and zero otherwise, and if $\vec{b}$ is a column s.t. $b_i = 1$ when $i \in B \subseteq [1,\ldots,n]$ and zero otherwise, then:
$$ M\vec{b} = (|B\cap X_i| : i=1,\ldots,m)^T $$
Since every subset $B \subseteq [1,\ldots,n]$ is represented by some $\vec{b} \in \{0,1\}^n$, $\mathcal{F}$ is a distinguishing family if and only if all the images $M\vec{b}$ are distinct, i.e. $|M\{0,1\}^n| = 2^n$.
The injectivity of multiplication by $M$ on $\{0,1\}^n$ is a weaker condition than having rank $n$, i.e. injectivity on all $\mathbb{N}^n$. A smallest binary matrix injective multiplication example with rank$(M) \lt n$ seems to be one like this:
$$ M = \begin{pmatrix} 1 & 1 & 1 & 0 \\ 1 & 1 & 0 & 1 \\ 1 & 0 & 1 & 1 \end{pmatrix} $$
which corresponds to distinguishing family $\{\{1,2,3\},\{1,2,4\},\{1,3,4\}\}$ of subsets of $\{1,2,3,4\}$.
Formulating the problem in matrix multiplication terms allows algebraic methods to be used. In particular a slightly different problem is considered in connection with Code Division Multiple Access (CDMA) systems in a 2009 paper by Sh. Dashmiz, P. Pad, F. Marvasti:
New Bounds for Binary and Ternary Overloaded CDMA
An explicit construction is given there for antipodal binary $m\times n$ matrices $A$ that are injective on $\{\pm 1\}^n$, where by antipodal binary we mean the entries of $A$ are drawn from $\{\pm 1\}$. Given an $m\times n$ solution, the construction provides one that is $2m\times (2n + m - 1)$.
Multiplication by any $m\times n$ matrix $A$ being injective on $\{\pm 1\}^n$ implies that it is also injective on $\{0,1\}^n$. To show this, apply the injective affine mapping $\vec{b} \to 2\vec{b}-\vec{1}$, so that if multiplication by $A$ of two distinct binary vectors in $\{0,1\}^n$ gives equal images, then already multiplication by $A$ of two distinct vectors in $\{\pm 1\}^n$ would have given equal images. The converse argument is similar, and henceforth we will refer to injective matrix multiplication without mention of whether $\{\pm 1\}^n$ or $\{0,1\}^n$ is the underlying domain.
Further: If $A$ is an $m\times n$ antipodal binary matrix with injective multiplication, then an $(m+1)\times n$ 0,1-binary matrix $M$ with injective multiplication can be formed from $A$ by appending a row $[1,1,\ldots,1]$ and using elementary row operations to clear any negative entries in $A$. Moreover the antipodal binary matrix can always be chosen to have already a row of all ones, so the need to add an extra row when converting from antipodal binary to 0,1-binary matrix can always be avoided.
Starting from a variety of $m\times n$ injective binary matrices, the ratio $\frac{n}{m \log_2 n}$ generated by the recursion $(m,n) \to (2m,2n+m-1)$ remains above $\frac{1}{2} \log_3 2$. However these recursive sequences have gaps in the $n$ values represented, and it is not yet clear that the bound can be established for all the intermediate values.