Need more details, and I'm not sure I got your question, but if I had to guess, you have pixel rounding on. If that's the case, you need to make sure that your object doesn't rotate or fall in a decimal coordinate. Otherwise, it will round to the nearest pixel, which can lead to some unexpected results/distortions.
Or another workaround is to work on a higher resolution and scale up your objects. This way there will be "subpixels" to accomodate non-pixel perfect coordinates and rotations.