I just put some notes in the About section.
One thing both sites I listed are in agreement about is that father Archibald didn't have a son named James, so I removed the (or James) notation on his name.
The contradictions are:
1) one site lists John as the son of Catherine Douglas and the other site lists him as his father's son by his second wife who was a Crichton. The same info already existed in father Archibald's About section but didn't connect the Crichton wife as this John's mother. There isn't any info in Archibald's About section to indicate proof of Catherine Douglas as this John's mother.
2) the second link states that father Archibald died in 1521 instead of 1529 as listed on his profile and, again, that info was already in the About section of Archibald's profile.
Archibald Napier, 4th of Merchiston
Anyway, lacking proof to the contrary, it seems this John is connected to the wrong mother.