Actually, that's the kind of government system we have, both position is elected by the people regardless what party they came in, it's the popularity vote. In the last admin both (Pres and VP) have different parties. This time, current admin different party too but signed an agreement to unite these parties "UniTeam" and then run as one, then both win. But sadly things got bitter for both started to show the stench of their political agenda, personality, and so on.
Doesn't really help when you're not saying which country it is and I have to figure it out, but again, you are wrong on your own issue.
Your president and vice-president were running mates, it doesn't matter what party they were if they chose to be allied, they were registered as the same alliance, what you were talking about being from the opposition would be a combination of Marcos and Pangilinan which obviously didn't happen!
So again, it's not inevitable at all, look at India, look at Argentina, and there are dozens more.