Lifting Up On Certain Blocks

For some reason some blocks with lift me up about half a block when stepping on them, but there's no slab there, in addition, even if I destroy the block and place it back the issue continues 

Even with stone, if I break the stone and place back the cobble, I still get lifted about half a block when stepping on it

At fist I thought it may be doors doing it, but it's not, the place where it does it the most though, is where I have 2 doors blocking water from flowing out of a water elevator
So maybe that has something to do with it? I have no real idea though, cause it does happen elsewhere
(Edit: I've attached an image of me standing on this invisible slab, as you can see, I'm eye level with the line in between the door and trap door, instead of the centre of the door)