3 possibilities :

1 - The angle between the photos is not large enough, Pixdim was able to reconstruct the 3D scene but calculations are somewhat approximate.
The final version of Pixdim will display a dialog box and change the point color to red.

2 - You may not have defined the reference scale, if this is the case, Pixdim uses a default value of 1 meter between points 1 and 2. Define a real measurement with the "Define Reference Scale" command.
Image

3 - You have measured 2D points positioned on 2D images. In this case you measure the distance in pixels on the images. Display a 3D page before starting to take measurements.