Unfortunately, it doesn't seem like a lot of folks are understanding what you're saying.
I don't normally pay that much attention, but I have noticed at times I've gotten a different number of penguins from one battle to the next when in a set of auto runs. Like I said, wasn't paying much attention and so I chalked it up to that, but it would be good to now what/if there's a reason for this.
It's not only the number of penguins that is weird, you also got twice the bookmarks and twice the stigma (12 per run), and possibly twice the catalysts too (?). And then, you also got 24 AP which is, I believe, twice the value of a run with AP buff. So maybe what happened is that you, for some reason got double of everything in 1 run. How/Why did it happen, that's another question but it definitely sounds like a glitch