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printf PLOUT "%.5f %.5e %.5f\n", $energy_bin[$i], $spec_cps[$i][$j], $
+sigma_cps[$i][$j];

use strict;
use warnings;
...
     $spec_cps[$j][0], $sigma_cps[$j][0],
     $spec_cps[$j][1], $sigma_cps[$j][1];
}

1.00000 5.00000e+000 15.00000 6.00000e+000 16.00000
2.00000 7.00000e+000 17.00000 8.00000e+000 18.00000
3.00000 9.00000e+000 19.00000 1.00000e+001 110.00000