[I posted this before hoping that it would spark a lot of conversation but unfortunately it didn't so I'll try one more time.]
I recently made a DNA test. My father was from Sierra Leone and I found out something quite extraordinary: from his side of the family I had 1% Papuan and 1% Native American from the Amazon. As we all know, these were not places from which people travelled to other countries or continents. How on earth could a Papuan from Oceania or an Amazonian from South America end up in Africa? These were all countries that were visited by the Portuguese who had slaves, right? Yet I'm not aware from which countries they had slaves from. I hope this will spark some interesting conversation. Thank you.
Depending on which data company you used to get the genetic analysis it probably means nothing. This isn't the venue to shame specific genetic data companies-- but generally speaking they have serious issues when it comes to non-Caucasian DNA samples, as they rely on very narrow sample sets from non-European peoples. So while they have good sample sets of the sorts of genetic variety/or ranges from European populations, they have very poor sample sets from elsewhere.
Therefor it's not surprising that you might have anomalies pop up when testing for an atypical North American/European branch of a family.
This could just as well be an indication of an African connection among those samples representing indigenous SA and Papua- which I would guess is more likely- but impossible to say as well.
Which company did you test with? As far as I know, none of the them are that specific that they can tell you Papuan or Amazonian.