> It's tough to know exactly what you're talking about without a screenshot, but set snap to grid to at least 1x1. This way, you won't be dealing with subpixels. Depending on your art style, you could also switch to point sampling in project settings. And, if you're unfamiliar, when you set the snap to grid settings, don't click off of the numbers until you've clicked back on the previous number entry box--otherwise, the values get reverted. You'll see when you try it.
See how it fades? the lining things up like that is irritating.
Also, snapping to grid now would require a complete level redesign, since some are alreday in subpixels and moving them doesnt just snap them to a whole pixel
That looks sort of like stretched out sprite objects. If it's just repeating/one-color stuff like that, use the Tiled Background object so you don't get stretching. If that isn't a stretched sprite, then I have no idea what would cause that other than something in your source image.