The force diagrams show the weights $W_A$ and $W_B$ of the blocks, directed down. $F_1$ is the force of block $B$ on block $A$, while $F_2$ is the force of $A$ on $B$. Reference:- An introduction to mechanics by Kleppner D And Kolenkow R
My doubt:- I am confused with $F_2$ and $W_A$. From where do this $F_2$ coming? Already $W_A$ is the force acted by $A$ on $B$ and $F_1$ is the reaction force.
You are jumping several steps ahead. The force diagrams keep $F_1, F_2$ and $W_A$ separate because they make no assumptions about the blocks being in equilibrium or about Newton's Third Law.
By applying Newton's Third Law, we can see that $F_1$ and $F_2$ are equal and opposite i.e. $|F_1|=|F_2|$. And if block $A$ is in equilibrium then we know that the net force on block $A$ must be zero, so $|F_1| = |W_A|$. If block $B$ is also in equilibrium then the net force on block $B$ must also be zero, so
$|N| = |F_2| + |W_B| = |F_1| + |W_B| = |W_A| + |W_B|$
as we expect.
Newton's Third Law will always hold, so we can always be sure that $|F_1|=|F_2|$. But the blocks are not necessarily in equilibrium. Suppose they are in a lift that is accelerating upwards at constant acceleration $a$. Then
$|F_1| = |W_A| + M_Aa\\|N| = |F_2| + |W_B| + M_Ba = |F_1| + |W_B| + M_Ba = |W_A| + |W_B| + (M_A + M_B)a$