The crux is the line

@singlefilter = pop(@filter)
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You create a new array containing on element, the reference to the poped array.

The line should read

@singlefilter = @{pop(@filter)}
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because you push references to arrays not arrays onto @filter (explicitly by using []) during the push, creating references to anonymous arays), and you couldn't do it any other way, because an array can only hold scalar values; a so called AoA is in reality an Array of Array-references!