
Is inkscape not capable of having the edges of the two objects lined up perfectly on top of each other?
Maestral wrote:When intersected or in other way trimmed, curves in IS tend to deform in a different fashion.
Proportionally, green circle`s outline is more affected with this intersection, more than the blue one - hence this slight difference.
p.s.
Use the Node tool to compare the both outlines.
p.p.s.
The difference is visible but even in the printing, it would most likely not appear. You may adjust the Preferences and the precision if needed.