score:4
What's the quickest way we can resolve this? Because it was not our fault but there was some mistake with the embassy issuing his days.
Also, I wanted to find out that since we have been dating for over a year now, are there any possible applications that can make his visa to be more than 90 days?
...
We honestly didn't check because he always visits and he always gets 90 days.
(My emphasis in both quotes).
If he's visited multiple times with 90-day visas in "over a year" (which I presume means less than two years), it seems quite likely that the shorter visa was not a mistake. ZA immigration are probably trying to limit his time to ensure that he's not effectively resident. If you want a longer visa then you may have to look at getting a residency visa: follow-up questions about that should be asked on our sister site expats.
Upvote:8
If the duration he was given was written on the visa then it was his fault that he overstayed because it was his responsibility to read that information.