Translation:Žofie has six fingers on her right hand.
With "in," it would mean that she is holding six fingers in her right hand...
A correct translation would have been: Zofie's right hand has six fingers. Since I am deaf to the intricacies of the Czech language, I cannot tell whether that is what the Czech sentence really meant.
Zofie's right hand has six fingers. = Žofiina pravá ruka má šest prstů.
The meaning is the same as the "Žofie má na pravé ruce šest prstů." but the syntax is different.