Appreciate the tag, but self-defense claims aren't really matters of law, but rather issue of facts. Assuming Nebraska doesn't have any unique language to their applicable statutes, lethal self-defense is justifiable when: a reasonable person in the defendants place would have a reasonable fear for their life or serious bodily injury (serious being really serious; ex: loss of limb or permanent disfigurement). The defendant bears the burden of establishing this defense by preponderance of evidence (more than 50%), while the prosecution only needs establish the elements of the crime.
So theoretically, a defendant can make a self-defense claim for anything. That five-year old gave you a dirty look? Maybe that bastard was mere moments from tearing you apart. There's nothing in the law that would prohibit that defense. It would just be an issue to fact as to whether or not you can convince the jury.
So going on what we have hear, I see the defendant, who's armed, get tackled, punches or a struggle occur, and a moment later a shoot. That's really a judgement call for the jury. As to why they a grand jury decided to indict despite the DA thinking self defense, I'm assuming the defendant either made remarks suggesting that he didn't feel his life was in danger (guy was a bitch and I was gonna kick his ass without issue) or perhaps the defendant escalated the situation by leaving to retrieve the gun. Don't know what was put before the grand jury.