The ones I remember:

Episode 5, 1st Mission: You come across a group of marines, including the drawling dude who ends up being your pilot for the rest of the season. They hijack a Phantom. I don't think a reason is ever offered why these guys were being kept alive.

Episode 7, 3rd(?) Mission: You rescue the Switchback Spartans from the cave. Again, no reason why these guys were captured, or why these presumably perfectly capable Spartans couldn't get out on their own. I think this one tied in to the first Harvester mission, where you track down Switchback team's transponder tags, which have all been erased. Why the tags were erased and left on the ground was also never resolved.

Episode 10, 1st Mission: A bunch of scientists are being held in the Harvester. These dudes actually explain that the Covenant were trying to get them to fix the Harvester (even though all it needed was a new battery). So this was the same deal as Jul Mdama hanging on to Glassman: his guys are just completely incapable of repairing anything, even Covenant tech. Doesn't make this new Covenant seem all that threatening...