Suppose I have two predicates $P(x)$ and $Q(x)$, such that $\overline{P(x)\wedge Q(x)}$ holds for all $x$.
Now, if $\displaystyle \bigwedge_{x\in A}P(x)$ for a set $A$, it must be certainly true, that $\displaystyle \overline{\bigwedge_{x\in A}Q(x)}$ by intuition. But suppose, that $A = \{\;\;\}$, then obviously both $\displaystyle \bigwedge_{x\in A}P(x)$ and $\displaystyle\bigwedge_{x\in A}Q(x)$.
Where is my mistake? I guess it is in the assumption that $$\bigwedge_x\overline{P(x)\wedge Q(x)} \rightarrow \left(\bigwedge_{x\in A}P(x) \rightarrow \overline{\bigwedge_{x\in A}Q(x)}\right)?$$
*Note: $\displaystyle \overline{P(x)\wedge Q(x)} \equiv \lnot(P(x)\land Q(x))$
$\displaystyle \quad\quad\quad\quad \overline{\bigwedge_{x\in A}Q(x)} \equiv \lnot \left(\bigwedge_{x\in A}Q(x)\right)$
Your intuition is based on the set $A$ having some nontrivial size. But as you note, the intuition is wrong if $A$ is empty.
You only need to change your intuition slightly. If $P$ holds for all $x \in A$, then we know that $Q$ cannot hold for any $x \in A$. That is, $\bigwedge_{x\in A} \lnot Q(x)$.
The mistaken intuition is in transforming $\bigwedge_{x\in A} \lnot Q(x) \ \ \ \rightarrow \ \ \ \lnot \bigwedge_{x\in A} Q(x)$. This step is only correct if $A$ is nonempty, but even then it is a weak step (for large $A$ the left hand side is a strong statement while the right hand side is relatively weak), so you would do best to forget about this sort of transformation — try to erase it from your intuitive repertoire!
The correct transformation would be that of De Morgan: $\bigwedge_{x\in A} \lnot Q(x) \ \ \ \rightarrow \ \ \ \lnot \bigvee_{x\in A} Q(x)$.