I'm betting the first problem has something to do with a difference in the consumable code section. Matter reconstruction, cauterize hull, and all other limited-use science powers use:
is_consumable = true
consumable_count = 1
The number is greater for the non-epic powers.
Kistler's Ague uses:
limited_use = true
use_count = 1
has_volley = false
can_be_disrupted = false
is_consumable = false
consumable_count = 0
Starbase Commander healing powers use the limited_use and use_count lines. This implies that Kistler's Ague should be usable once per battle. I have no clue why the stored number is off. (And when I say should, I mean code wise, not developer plan wise.)
As to the second part: which enemies have resisted the effects, and which effects did they resist?
Third part: based on my experience with absolutes and percents getting confused, that's probably a bug.