DF Classic had a quirk where some items don't fit into the female variant hands:
While the bug was present in DF Classic, DFU seems to further displace these items for both hands. My theory is that the "male" variants of the weapon textures (and as such their programmed visual off-sets)are being used incorrectly on female paperdolls. There should be 4 distinct "body types", and each of those have male and female variants. There are some other issues with helmets as well that have been reported to me, so it'd be worth looking over that whole area of code.
If it helps for testing, find included a copy of upscaled textures: these were generated directly from DF Imaging 2, and appear to have correct dimensions and labels.
I think the problem is the hilt of the sword. The hand, it's not around the hilt, but inside
Not quite. Oddly, though they (OG Creators of DFC) developed a masking solution for hats and cloaks, they decided not to use that for the weapons, instead opting for just cutting out an area on the weapon in the exact spot the hand would be, and drawing the weapon over all other layers (at least I think so).