It happened to me many times and after some research, I found that those pictures were not aligning because I wasn't pivoting the camera on its lens nodal point.
So, if the answer is to pivot the camera on the nodal point, the answer is simple, correct?
Well not quite...
The first problem is that, in reality, there are two nodal points: the front nodal point and the rear nodal point. The physics associated with this fact, are way beyond me. But for our purposes, we will be talking about the rear nodal point.
Second, you will need to find this magical point which changes from lens to lens. As you change lenses, the nodal point changes.
Also, when using a zoom lens, there will be a nodal point for each focal length. If you change the zoom from 50mm to 35mm, you have also changed the nodal point.
Third, assuming you know exactly where the nodal point is for a specific focal length, you will need to pivot the camera on it and not on the contact point of the camera to the tripod head..
For all those reasons, and many others, I would recommend not to worry about the nodal point unless you are making a living shooting panoramas or high precision 360 degree views.
For the average person that shoots only landscapes/seascapes where all subjects are all far away, I would say, forget the nodal point discussion and just enjoy shooting your panoramas.
The actual process of measuring the EXACT position of the nodal point is such a "pain in the neck", that I will not even attempt to describe how to find it.
See links below how to do it...
So, if you don't know where it is located and still want to take a crack at it, how do you solve this issue? This is how I solved it:
I cheat: I use a table
There are almost as many theories how to properly measure the nodal point as there are photographers. There are scientific methods, there are home brewed solutions, and there are combinations of both like this one, that will give you astoundingly accurate measurements.
There are also several published tables that cover some of the more common lenses.
See links below...
I only use one lens
When shooting close and far subjects I always use the same lens: a Nikon 50mm f1.4 lens. One lens, one measurement and I'm done.
I use a panorama bracket
If you look at this image ...

you will see that the natural pivot point of the camera needs to be moved backwards so that nodal point can be over the tripod head's pivot point.
This is accomplished by using a bracket that, on the bottom, attaches to the tripod head and on the top has an adapter, that the camera gets attached to. This adapter slides backwards and forwards to allow the photographer to properly position the camera until the nodal point is over the pivoting point of the tripod head.
Once the bracket is properly installed and aligned, it will look something like this:

So how does the bracket work? Looking at first image, you see that the camera was positioned in a conventional way over the tripod head. Any pivoting that takes place, happens at the contact point of the camera and the head.
In next image, the camera is no longer attached directly to the tripod head but instead attached to the blue adapter that slides on the red bracket.
This is a fairly inexpensive and ingenious solution that solves the issue of having the nodal point of the lens over the tripod head pivot point.


Once you have one of those brackets, and have properly positioned the camera, you will end up with perfectly aligned images that will produce magnificent panoramas...
Well... are you ready for this?
Even if you think you have everything perfectly aligned and you have the camera pivoting exactly where it is supposed to, you still may end up with parallax errors.
This is because many cameras have the point that attaches to the tripod, not in line with the natural axis of the camera. Look at these images and you understand the issue.
Because of modern cameras being loaded with so many electronics, the final location of the attachment socket, ends up being sometimes an afterthought.
Click the images to see them in larger sizes.
Misaligned cameras...

Properly designed cameras

If you have a camera that has that issue, you need to select a bracket that allows the camera to be adjusted both longitudinaly ( back and forward ) and transversaly ( side to side ).
Off course the perfect solution is to just buy a specialty panorama camera. Unfortunately they are beyond what my "home CFO" is willing to approve...
How to find the nodal point
Finding the Nodal Point of a Lens
Nodal Point Alignment
Panorama Imaging
Digital Grin
Determining the Nodal Point of a Lens
Nodal point tables for common lenses
Entrance Pupil Database
Lens Measurement Table
KingPano
Brackets and pano tripod heads
Real Right Stuff
Home-made panorama head
The Nodal Ninja