Start with a sheaf $\mathscr F$ on $X$, and then take $F:=\text{res }\mathscr F$ to get a sheaf on the base $B$. We'd like to extend this sheaf back to all of $X$ and see what happens. Well, now you should go look how this extension is constructed in Vakil. It is a large construction using classes of "compatible germs of $F$", so it is certainly not **equal** to the original sheaf $\mathscr F$. The two are **isomorphic** as sheaves on $X$, however.