The subtlety in putting two identical mesons in the "same state" is that not only are the mesons indistinguishable from each other, but they aren't well-defined composites at all: We can't say which quarks are paired together.
Given two up quarks and two anti-down quarks, we can make two $\pi^+$ mesons, but they can equally well be $u_1 \bar{d_1}$ and $u_2 \bar{d_2}$, or $u_1 \bar{d_2}$ and $u_2 \bar{d_1}$. The two-meson state must contain both possibilities (with opposite signs since they differ by one fermion exchange).
So the closest thing to putting both mesons in the "same" one-meson state $f$ would be $F = f(u_1 \bar{d_1}) f(u_2 \bar{d_2}) - f(u_1 \bar{d_2}) f(u_2 \bar{d_1})$. This is symmetric under meson exchange (simultaneous exchange $u_1 \leftrightarrow u_2$ and $\bar{d_1} \leftrightarrow \bar{d_2}$).
If two identical mesons were simultaneously at the same quantum state, there would thus be two pairs of identical quarks in the same quantum state, right?
No, there is no inconsistency because the quarks are generally entangled and not in well-defined individual states; we do not obtain $F = 0$ except in special cases like $f(u \bar{d}) = g(u) h(\bar{d})$.
A simple example in operator notation, neglecting degrees of freedom other than spin: The one-pion state is $(u_\uparrow^\dagger \bar{d_\downarrow}^{\!\dagger} - u_\downarrow^\dagger \bar{d_\uparrow}^{\!\dagger})|0\rangle$. So with two pions we have
$$(u_\uparrow^\dagger \bar{d_\downarrow}^{\!\dagger} - u_\downarrow^\dagger \bar{d_\uparrow}^{\!\dagger})(u_\uparrow^\dagger \bar{d_\downarrow}^{\!\dagger} - u_\downarrow^\dagger \bar{d_\uparrow}^{\!\dagger})|0\rangle = -2 u_\uparrow^\dagger u_\downarrow^\dagger \bar{d_\uparrow}^{\!\dagger} \bar{d_\downarrow}^{\!\dagger}|0\rangle \ne 0.$$