Even though the option After nesting center graphics on sheet is toggled on, the graphics are not centered on the last layout (or some layouts).
You will see that there is a green recycle symbol (Offcuts symbol) placed in the problem layout(s). This symbol means i-cut Layout has created an "offcut" area and this overrules the center option (to maximize the size of the offcut area).
This is not a bug but normal behavior.
If you don't agree with this overruling, you can change the Offcuts value in the Preferences of i-cut Layout.
The setting to adapt is the Minimum Width or Height.