I have created an assembly where a diameter 24 mm bolt is passing through many parts each having a dia 24 mm hole. There is a circular pattern of theses holes and bolts. This arrangement When I check for interference between the bolt and each of the parts, it shows that there is a very thin interfernce surface on half the perimeter and an air gap on the remaining half on all the parts through which the bolt is passing. I am not sure if this will work if I want to create a mesh on the parts to do a flow analysis.
Are you sure that all Ø24mm holes are perfectly round? I have had the same problem when I projected circle sketch to a curved part and the resulting hole was tiny bit elliptical instead of a perfect circle. That way the arcs of the ellipse have different center points which could lead to wrong positioning of the bolt the same way you described.
You are right. I had indeed zoomed and check the holes and they were clearly not perfectly roung and an interference could be expected. I tried recreating a new part but to no avail. So, instead, since I had another part of different features but the same hole pattern and that was fitting in well, I modified that parts other features to create the required part and upon mating it worked fine with no interference. Lucky me, I had that part. It is working fine now.