Why were some of my contacts automatically merged without notice? I found several questions here where people want to merge several of their contacts into one.
I'm having exactly the opposite problem:

On both my Android devices (Google Nexus 4 and Nexus 7), two of my contacts were automatically merged, without noticing or asking me first.

I noticed this when I didn't find my mother anymore in my contacts. After some searching, I found that my father's entry now had two cell phone numbers (his own and my mother's) and two dates of birth (again, his own and my mother's).

Now I understand how it's possible that they were recognized as "similar" (both share the same last name, street adress, non-cell phone number and e-mail adress), but it's beyond me why on earth it would just merge them automatically, without any notice?

Please note that they are still two separate contacts in the GMail web interface.
They are just merged in the contact apps of both my Android devices.

I had another Android phone until a few days ago (HTC Wildfire with Android 2.2), but I don't know if they were already merged there too or if this is a new bug in Android 4.2.

Finally, I compared my complete contact list on my phone with the one in GMail, on order to find out if more contacts were merged.
But my parents were the only ones, even though I have a few more married couples with the same names and adresses in there.

Any idea why this happens and how I can separate them into two different contacts again?
I found a solution that kind of works, but IMO it's still unsatisfying.
After some googling, I found that this is a known bug in Android.

Apparently it's fixed (the issue is closed), but I don't think so, because not only do I have these problems now, there are also comments with complaints which were posted after the date when the issue was closed.

One of the comments had a solution that works for me, but it's not ideal:

When I edit the contact (which has my father's name, as mentioned in the question) it shows both contacts to edit...still on the same screen, but clearly separated as different contacts.

On this screen, I can separate or merge them in the options menu. When I choose to separate them, they become two different contacts again...but only on this device. I have to repeat that on the other device in order to separate them there as well.