I make most my panoramic photos using photomerge in Photoshop. Normally it works super good without any problems but sometimes I just have to sit there and scratch my head with what it outputs. This first photo for example: 3 vertical images with a Nikon 85mm tilt-shift lens. In other words, it should go together absolutely perfectly, without any distortion or misalignment anywhere. What happened in photomerge? A great mystery of life. All I can think of is that the clouds may have given it some problems. I just had to use the old fashioned way and combine it by hand. No problem.
Interesting results on this second photo as well. And again, it was simple enough to align and blend by hand for a perfect result.