Just put your scores into an array and calculate the average using List::Util sum in a second loop.

use List::Util qw(sum);

use strict;
use warnings;

my %scores;
while (<DATA>) {
    chomp;
    my @fields = split ',';
    push @{$scores{$fields[2]}}, $fields[3];
}

for my $student (keys %scores) {
    my $average = sum(@{$scores{$student}}) / @{$scores{$student}};
    print "you bad boy, $student, $average\n" if $average < 50;
}

__DATA__
XY,50,weret,30,reewrw
XY,25,weret,30,rerwe
yz,45,ferr,55,rwree
YZ,90,ferr,55,deert
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