The error lies in the fact that you are incrementing $j here:

$athlete[$i][$j++] = $bug;
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The problem is that since $j is one larger than before, and thus you are not printing out the same thing (2 lines later) as what you just set. (ie $athlete[0][0] != $athlete[0][1]) so you get the warning.

you might want to increment the $j by one at the end of the loop.

update: I am afraid, I might have confused you so here goes. Let's pretend we are going through the inner loop on the first pass:

$j = 0;
foreach my $bug (@row) {
  #here $j == 0; so the following line would be
  #$athlete[$i][0] = $bug;

  $athlete[$i][$j++] = $bug 

  #at this poing the $j == 1 because of the $j++
  #on the previous line.
  print "\$i\$j is assignt $i:$j\n";
  print "\@athlete[\$i,\$j] is assigned the value $athlete[$i][$j]\n";

  #on the previous line you $j == 1 so you are refering to
  #$athlete[$i][1] which is not the same as what you set
  #but rather the value you will set the next time through.
  . . .
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if you change the print line to:

print "\@athlete[\$i,\$j] is assigned the value $athlete[$i][$j-1]\n";
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you would print the value you just set, which is what I think you are trying to do.

-enlil