Oof...can't believe this one slipped past me as well...I have implemented a fix, and will put out a patch next week (once I have had time to run some more tests). One of the joys (?) of being the designer AND the only play tester is that you can never quite think of all the ways to do everything...
Regarding your other question, it IS possible to complete the "Retaking Tocamllo" quest with a better outcome than the one I think you are getting...see below if you don't mind SPOILERS!
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When you first enter Tocamllo with Elam, don't enter the office building right away. Instead, walk just past the building and look up near the outer wall of the city. There, you'll see a fallen Steel Legion Gunner. Talk to him, then head into the office. Next, check all of the bodies on the first floor of the office. One of the Steel Legion Specialists is still alive, and you will need to talk to him as well. Once both the Specialist in the office and the Gunner outside have been saved, head upstairs and talk to the sergeant as normal. He should make a comment to the effect that they don't have many men, but at least Elam has enough for a full squad.
Once you head back out to defeat the rebels, you should be able to find a total of four (4) rebels hiding in various spots around the ruins (stepping into their line of sight will cause them to attack you). In addition, there are two (2) non-hostile rebels in the ruins: one is talking to Nathan, partially obscured by a tree next to the large house across the street from the white office building, while the other is hiding behind a car in the bottom left corner of the ruins. Talking to each of them will cause them to leave the area quickly (find them again in Pedregal Springs for extra rewards).
Now, you're ready to face off against Felix and finish the mission! The aftermath of the quest should be quite different now...
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SPOILERS END