The order in which you assign stuff is wrong. Getopt::Std removes items from @ARGV. Try

#!perl
use 5.020;
use Getopt::Std;

@ARGV = ("-u", "my miscreants", "Some reason");
my %opts;
getopts ('u', \%opts);
my ($miscreants, $reason) = @ARGV;

say "---";
say "Miscreants: $miscreants";
say "Reason: $reason";
say "-u set: " . $opts{'u'};

%opts = ();
@ARGV = ("-u", "my miscreants", "Some reason");
($miscreants, $reason) = @ARGV;
getopts ('u', \%opts);

say "---";
say "Miscreants: $miscreants";
say "Reason: $reason";
say "-u set: " . $opts{'u'};
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