Your code, as posted, works just fine for me. If you want, you could list assign the results from the coefficients method. Might make things a bit more self-documenting:

use strict;
use warnings;

use Statistics::LineFit;
my $fit = Statistics::LineFit->new;

$fit->setData(
 [qw[ 1 2 3 4 5 6 7]],
 [qw[ 2 3 4 5.5 6.5 7.5 8.5]],
) or die;

my ($intercept, $slope) = $fit->coefficients;
printf "i=%.4f, s=%.4f,  R2=%.4f\n", $intercept, $slope, $fit->rSquare
+d;

# or

return ($fit->coefficients, $fit->rSquared);
[download]

Maybe you're calling your function that does this stuff in scalar context, and thus flattening the return list? What exactly are you getting back?