In Image 1, just above the calcification there is a tiny patent ductus arteriosus, seen best on the lower set of 3D reconstructions. The calcification appears to be in a very shallow ductus diverticulum that leads to the PDA itself. Presumably there is something dystrophic about the aortic wall in this situation which has led to the calcification or which has predisposed to an atheromatous plaque.
Image 2 is an old patch repair of a perimembraneous VSD. The calcification is in the patch. This is not at all unusal. Note that the pit of the VSD is still present as the patch was applied to the right ventricular side of the defect.