I have noticed a kind of contradiction arising due to set-builder form involving universal set$(U)$ while I was performing operations on set theory.
Here it is -
Let us consider an arbitrary non-empty set $B$. Then, $B = \{x : x \in B\} = \{x : x \in B \wedge x \in U\} = \{x : x \in B \cap U\} = \{x : x \in U\} = U$
But this is contradiction as $B \not= U$. Instead $B \subseteq U$.
Is it really a contradiction or my misconception ?
A detailed explanation would be helpful.
As has been explained in the comments (and if one of the original commenters adds an answer, I'll delete this one), the error is not a subtle logical issue but rather an intersection calculation.
You ask,
Well, the answer is: the first one is not necessarily true given our hypotheses on $B$ and $U$, while the second one is necessarily true given those hypotheses. I suspect the special character of $U$ (= the universal set) is making this more confusing than it should be.
Forgetting about universal sets, remember that whenever $X\subseteq Y$ we have $X\cap Y=X$, but we do not necessarily have $X\cap Y=Y$ (indeed, we won't unless $X=Y$). For example, take $X=\{1\}, Y=\{1,2\}$; we have $$\{1\}\cap \{1,2\}=\{1\}\quad\mbox{but}\quad\{1\}\cap\{1,2\}\not=\{1,2\}.$$
Of course the universal set does pose serious issues, and the usual choice of axioms for set theory in fact prohibits such an object (although some other set theories allow it at the cost of weakening other axioms); but that's irrelevant to the particular issue here, which is really just an issue with subsets and intersections.