Shadows that are not supposed to be there

There are areas about 6 block in diameter around my village and nowhere else the areas seem to be a shadow despite there being no structure above it to make the shadow, the shadow did not seem to go away if i put a torch in or near it I tried cycle render distance but to no avail until I went in and then out of the nether portal then it started to work again, it started after I got out of the nether portal for some reason when I opened the door in my house only the half I hovered opened while the other didn't and when I tried to open then other half it wouldn't and also for some reason before I went in to the nether the hostile mobs wouldn't spawn even though I was in normal mode and the only hostile mobs that would spawn was the pillagers the crossbow and the axe ones but after I went in and out of the nether every thing started to work again. (I had to enhance the image so it would be easier to see.)