It seems that when I scale solids, if it's not a round number like 50% or 25%, the edges start to blend and it becomes difficult to line them up together, it might also not look nice when working with alpha footages. How do I prevent this problem when I want to scale them freely?
If you want to easily adjust rectangles to whole-pixel increments, I suggest using shape layers instead of solids. You can specify the size of a rectangular path directly in pixels.
If you really prefer to use solids, add a Scale keyframe, then double-click the keyframe icon to open the Scale diloag. Change the units from "% of source" to "Pixels", and enter whole values in the text entry fields.