Your use of SQUARE BRACKETS causes the arrays to contain a single element.
That element is a reference to an array.
Since you are beginner, it would seem that this structure is not intentional.
Also, you have not posted what code you are running to compare the arrays and extract unique elements. By the way, the algorithm to do this is covered in the perl documentation FAQ.
It is difficult to suggest a course of action other than to gently request you to please RTFM,and read How (Not) To Ask A Question.
Update: The OP has modified the node, and replaced square brackets with parens, and added code, since this response was posted.
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