Yes, it is supposed to be one Sample per battle. Sampling after a fight on one floor and before a fight on the next are effectively the same, so I only allow one round of either per fight. That way, there's no frustration when you go up stairs and realize you forgot to Sample.
As for more Endless Challenges, these haven't quite been implemented yet. However, a Hard Endless Challenge will likely be added in the update after 0.3.6, and unlocked after the Main Story content in 0.3.6. (And eventually, an even harder one is planned for the post-game...)
I'm not sure what might've happened, but Malixinne's Block and Dark Stone can shave off 43 points of damage on their own, so it's possible you might have hit her when she was blocking the first time. And if you went from a Defense Focus oriented strategy to an Attack Focus strategy, combined with Power Booster increasing your total Attack by 50% of its base value (or straight-up doubling it if you used a Super), which gets multiplied further by the Overcharge? I can easily see that adding a huge increase in damage. Overcharge is incredibly powerful if you can safely use it. (That's the trick, of course- safely using a 65%/85% item and then immediately using it to attack instead of blocking or healing isn't always easy.)
EDIT: Almost forgot to mention the rumble. I just realized a "Fadeout BGS" command was missing on one page of the move events in the Grove. That should be fixed with the next update!
