The standard formula is
$$P(B|A)=\frac {P (A \cap B) }{P (A) }$$
Thus, $P (A)=P(B | A) \,\,\,$ implies $$P (A \cap B) =[P (A)]^2\,\,\,$$ and not $P (A)=P (B)\,\,$.
For example, consider a Venn diagram where there is one circle representing $P(A) =0.2\,\,\,$, a second circle representing $P (B) =0.9\,\,\,$, and where the two circles overlap in a relatively small region whose area is equal to $0.04\,$. In this case, we have
$$P(B|A)=\frac {P (A \cap B) }{P (A) }=\frac{0.04}{0.2}=0.2$$
and then $P (B|A)\, $ is equal to $P (A) \,$, but clearly we have $P (A) \neq P (B) \,\,\,$.
In other words, the problem in your considerations is when you conclude that, if $P (B|A) =P (A)\,\, $, then $B $ must exactly overlap $A$. In fact, the condition that $P (B|A)\,\,$ is equal to $P (A) $ only tells us that the ratio between the area of the intersection of the two circles and the area of the circle representing $A $ is equal to the numerical value of the circle A. It does not tell us that the intersection area or the area of circle $B $ have to be exactly overlapped with that of circle $A $.