Please make sure that you marked each vertex on at least two images in order to orient the model. When a polyline or a surface is created, next to the measurements "error n/a " appears, indicating that the measurement accuracy cannot be calculated till all the vertices of the Object are marked on at least 2 images. You can find more information https://support.pix4d.com/hc/en-us/articles/202560609.
After the vertices are marked in the images, the model has to be reoptimized. The Reoptimization should orient correctly your model and then your outputs should have the correct orientation.
Note, if the project has images with geolocation and the Orientation Constraint is too different from the orientation given by the image geolocation, the Orientation Constraint will not be taken into account. If the orientation given by the image geolocation is inaccurate, the geolocation should be removed to orient the project. For more information about the image geolocation: https://support.pix4d.com/hc/en-us/articles/202557639#gsc.tab=0.
For more information: https://support.pix4d.com/hc/en-us/articles/205360385.