Different results from merged and original dataset

[Genetics189291]

Original dataset model fails for both and then on merged dataset one sample passes. Should I be worried for any future results 

Also is their a fix for this because I followed all the steps, so I don’t think anything went wrong with the merging

[Kale]

Did any of the left or right populations have samples added as a result of the merging?

For future consideration; I keep a datasheet of outgroup F3 stats, and every time I merge a dataset I rerun a couple from that sheet to make sure they match.

[Genetics189291]

Did any of the left or right populations have samples added as a result of the merging?

For future consideration; I keep a datasheet of outgroup F3 stats, and every time I merge a dataset I rerun a couple from that sheet to make sure they match.

Not that I can see, the only sample I added to the dataset was my sons when merging and nothing else changed in the left and right as a result of the merging ran the same exact left and right but different results. 

Is this due to using merge it? I can take you through my steps