Hi Bartosh, I've attached here a reconstructed version of your object which has the pieces aligned, it should now behave better when you do the boolean difference, the cutting object will leave its "imprint" into the base object sealing up that hole area automatically.

I rebuilt this by extracting the edge curves from the flat face, tuning up the control point alignment that I mentioned above so it was smooth on that upper part, then extuding that, then using the edge of the extrusion to do a 180 degree revolve, then boolean union of those 2 pieces and also with the bottom knob which I had also extracted out.

Somehow during your construction you ended up with a slightly different profile shape for building the revolve portion versus the extrude portion... Make sure when you're picking things like revolve axes that you have snaps turned on including "Straight snap" so that you can easily get exactly vertical and horizontal lines.

- Michael