Using whetstones on invalid targets seems to deplete usages. Is it possible to change that?

Also, are you supposed to not be able to just target yourself, or is that a result of my dual-wielding at the time of usage?

Right-handed SLASHING weapon should work for ya.

It won't work on your heavy flail.

You have to use it on your blade. (Slashing/piercing weapon) - not on yourself. Using it on items will likely continue to deplete charges, as it's pretty much the case for every Charge/use item (Also to prevent exploits)

*uses whetstone on flail*

Hah, now my flail is... Sharper?

You've used the whetstone at this point, and it was a stupid thing to do so on the flail, you lose a charge. I don't see what the problem is.

Hmm, there are weapons which could surprise you with their type, like daggers, etc. (I think Dagger is piercing)

I didn't use it on a flail. :( It was rapier/shortsword, and none of them were affected (both piercing).

it should work on piercing weapons too. Tarfil uses one on his shortswords

Seems not, last time I checked (though it was long ago)