You can double check whether the template was right or not by measuring from those points to the center line you should have scribed on the frame (assuming you were following the directions).
The instructions have you test fit the crossmember to the measured/scribed points and clamp it in place to ensure the holes are in the correct locations relative to that line.
Before jumping to any conclusions, I would take the crossmember back out, remeasure that scribed line, measure from it to the bolt holes you drilled on both sides, and measure diagonals on the frame to identify the actual source of the issue.
