When one passes from cohomology to homology, the wedge product of differential forms becomes the intersection
product. That is, if $N_1$ and $N_2$ are submanifolds of a smooth manifold $M$, and $N_1$ and $N_2$ are transverse,
the intersection product of the homology classes represented by $N_1$ and $N_2$ is the homology class of $N_1\cap
N_2$, which is also a submanifold by transversality. However, unless one takes mod 2 homology, one must choose
orientations on $M$, $N_1$ and $N_2$ and consider the homology class of $N_1\cap N_2$ as an oriented submanifold.
The sign change you're asking about comes from these orientations; specifically, the two intersections will be
oppositely oriented, and therefore will differ by a sign.
A quick note about the intersection product is that it reduces dimension: this is because Poincaré duality
exchanges $H^2(T^2;\mathbb R)$ and $H_0(T^2;\mathbb R)$, and exchanges $H^1$ and $H_1$, so the cup product
$H^1\times H^1\to H^2$ is sent to the intersection product $H_1\times H_1\to H_0$. This is why the dual to $\mathrm
dX\wedge\mathrm dY$ is the homology class of $S_X^1\cap S_Y^1$ in $H_0$, not $S_X^1\times S_Y^1$ in $H_2$.
Now the computation. Let's orient $T^2$ in the usual way, so that $(\partial_X, \partial_Y)$ is a positively
oriented basis of the tangent space at any point. $S_X^1$ and $S_Y^1$ intersect at a single point, and do so
transversely. The orientation convention for an isolated intersection point $p$ of oriented transverse submanifolds
$N_1$ and $N_2$ of an oriented manifold $M$ is that we count that point as $+1$ if the orientations on
$T_pN_1\oplus T_pN_2 = T_pM$ agree, and as $-1$ if they disagree. In our case, when we consider $S_X^1\cap S_Y^1$,
the orientation on $T_pS_X^1\oplus T_pS_Y^1$ is the usual orientation, which agrees with the ambient orientation on
$T_pT^2$, so the intersection number is $+1$. For $S_Y^1\cap S_X^1$, we obtain the opposite orientation, for which
$(\partial_Y, \partial_X)$ is positively oriented, and therefore the intersection number is $-1$. Letting brackets
denote homology classes, this means
$$[S_X^1\cap S_Y^1] = -[S_Y^1\cap S_X^1]\in H_0(T^2;\mathbb R).$$