One of my three Habrosus Cory Cats died.

I saw all three of them scurrying around, apparently happily, and eating Friday night (April 4). I saw no sign of illness. Then I noticed for two days and nights in a row I only saw two of them. That seemed unusual but it hasn't been uncommon to only see two at a time because they're so tiny and they have hiding places. I was worried, though, especially after seeing ammonia at .25 and sure enough found one dead last night (April 7). I think it had been dead for at least a day and I think that's probably the reason for the ammonia reading.
I've had them for about two months. They're still babies, about 1" long. (Habrosus are pygmies and only get to about 1-1/2".) They share a 6-gallon filtered and heated tank with a female Betta.
The temp is about 78 degrees. As far as I know, that's on the upper end of the scale for Habrosus, but acceptable.
My water readings since I got them have almost always been 0 for nitrites, nitrates and ammonia. The tank was cycled when I added them. There were just a couple of exceptions: one an almost unreadable trace of nitrite, and one about 3 ppm nitrate, both more than a month ago. (I don't know why the nitrates are almost always 0. I change about 25% of the water, but only every couple of weeks because of the 0 readings. Could this be the problem?) I use an AP test kit and test about twice a week.
I suppose it's possible the Betta killed it. That doesn't seem likely to me, though, because she's been a very good girl with them as far as I know. Besides an initial period of a few hours of her chasing them and nipping toward them (not actually nipping), I've not seen her do anything more than mildly chase them away when she's stealing their food. I know Bettas can seem mild-mannered toward the kind of tankmates that are usually considered compatible and suddenly turn, but it just doesn't seem like her to do that. She's just ignoring the two Cories today as usual, which also seems like a hint that she's not turned into a Cory-killing machine. I introduced her to the tank after the Cories.
Could it be a disease? What diseases can Cories get where there are no outward signs and then the next day or possibly two days later they're dead?
I read through
this thread called "Help! Cory Cats on death row." It seems Trio123 was losing her Cories suddenly and without warning. I wonder if there could be a same or similar cause, although a cause has not been identified in that thread as of now.
I'm sorry this post is so lengthy, but I wanted to give you as much info as possible. I'm desperately hoping someone will have a good guess gleaned from some hint here as to what went wrong or what I can do to help save the other two cuties from the same fate.