I think you're wondering why there is a darker area where the two circles overlap?
If you place a semi-transparent object above another, naturally the lower object is going to show through. If you have two semi-transparent objects, the area where they overlap is also going to be affected, since neither object is fully opaque.
What you want to do is leave the colour opacity of each object at 100% and change the layer opacity. This affects every object on the layer, and how these objects interact with other layers, but it doesn't change how objects on the same layer interact with each other (so 100% opaque objects on a layer are still opaque in relation to each other.)
I've thrown together a quick graphic to demonstrate what I mean. In Image A, each circle has its opacity reduced to 50% and you can see the dark overlap. The layer itself is at 100%. Image B has the circles at 100% opacity, but the layer is 50%. As you can see, there's no overlap.
Finally, if you're new to Inkscape, be aware that there are a couple of ways to change the opacity of an object (you may know this already, but just in case!) You can use the slider that I've pointed to Image A to adjust transparency, but you can also change the alpha value in the colour itself. In the Fill and Stroke panel, look at the colour blocks labelled 'R', 'G' and 'B'. Underneath those is another labelled 'A'. You need this to be at 255 for the colour to be fully opaque.