You don't need to set arrays to empty at declaration time - they start out that way.

Rather than using shift to pull off parameters one at a time in various scattered locations through your sub, use list assignment with a declaration of a list of variables at the top of the sub.

If you have a reasonable variable name adding a comment that simply reiterates the variable name in expanded form doesn't add any information.

Taking all that into account your code sample becomes:

my @isec;
my @b;

(@b, @isec) = ArrayFunctions(\@ArrayA, \@ArrayB, \@b, \@isec);

sub ArrayFunctions {
    my ($a_ref, $b_ref, $b, $isec) = @_;
    my @a = @$a_ref;
    my @b = @$b_ref;
    my %Aseen = map {$_ => undef} @a;
    my %Bseen = map {$_ => undef} @b;
#.......... Other Code .....
}
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Oh, and misleading comments are worse than no comment. There was a mismatch between the names of the hashes in the sub and the comment so I removed the comment. If the comment was right and names are wrong, change the names (and still omit the comment).