You used the transform tool to scale?
This is pure conjecture, I’d have to try it later, but:
Getting an exact pixel size by hand is challenging, and the scale option at the docker isn’t your friend in this case because it only works for round % numbers and the closest, 11%, yields 636.63636363(…) px.
Meaning Krita won’t know what do with that fraction. Afaik it is possible to have fraction of pixels, and where and if they’re rendered depends on the layer position.
It could be that it isn’t the act of moving the other layer that’s triggering the issue, but finishing the action of moving by changing tools, so Krita updates the layer size, the canvas, and now the layer is left enough the pixel is rendered, it counts for position. You correct it, now it isn’t, the position changes again after once you’re done, and it goes on.
I’ll try to reproduce this later today.
Related tips
You can move layers by a pixel using the transform tool + keyboard arrows.
There’s also a docker, Arrange, with which you can align layers. Not paint or file layers (I’m not sure how you imported your images), but I wrote a plugin that can arrange those and do a bit more.
Direct link: GitHub - Cellosia/krita-arrange-2: A plugin adding support to aligning and distributing all types of layers
Thread here at KA: Arrange 2: Universal alignment tools for all types of layers
Please read about the limitations, it can’t undo/redo because it’s only a plugin but I guess it’d still help you a lot. I know I use it all the time. 