When inserting two flanges at the same point, model graphics looks as if there is only one flange modeled (see left image) instead of two flanges (see right image).
AutoPIPE flanges are modeled as a single point graphic. Sometimes when adding the 2nd flange, is is graphically shown over the first flange give the appearance of only a single flange. However, as you can see in both images above, there are 2 flanges modeled at the same point.
The CAE development team is working on a new enhancement (CAE-CR-941) to model flanges as 2 points components. Until such time, as long as there are 2 flanges correctly located to account for the correct weight, ignore the graphics. Both images above would be correct.