In Agua Verde, there are two main missions to inevitably take out an HVT. Before doing the first, I went to the location where it turns out the second mission takes place as I was going to pick up the weapon in the compound. Once I was in what I later found to be the mission's zone, my character gave the information about finding the HVT and eliminating him, yadda yadda. I was even able to sneak up on the guy that turned out to be the assistant and kill him.

But even after everyone was dead, nothing counted as I had not completed the first side mission. So it seems the bug is either that the character lines were triggered by the designated mission area prematurely, or the bug is there was no mission complete even though I stumbled upon the guy they were able to identify as the HVT we were after (I assume the former).

The HVT was there in the second take of the mission so luckily no issues came up