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The grid unit is 1 pixel.
Below is two overlapped rectangles:
Underlying one has blue fill color an black outline color. Also it has Align Stroke to Inside setting:
As you see, it also has stroke weight set to 1px.
Nevertheless, the overlapping rectangle, which has no outline and blue fill is obviously slightly bigger.
Also, according to the grid, it is evident, the outline of the underlying rectangle is thicker than 1 px.
How can I fix this?
You can achieve the desired result by making sure that you have de-selected the option for aligning all objects to pixel grid in the document setup.
From your image I'd suggest the rectangle with the black stroke isn't actually smaller, it just appears that way because of the black stroke.
