How to reproduce:
1. Open the attached "RectTransformsBug" project and open "Primary" scene
2. Enter playmode
3. Press "Press Me" button twice to enable and disable nested Canvas

Expected result: Nested Canvas is disabled and enabled, child Canvas Rect Transforms doesn't change
Actual result: Nested Canvas is disabled and enabled, child Canvas Rect Transforms are changed and they are scaled along the entire parent Canvas onto each other

Notes:
1. The issue can be reproduced without entering playmode, just disable "Canvas" GameObject in the Inspector (the one that contains "CanvasPool" prefab) and re-enable it
2. You can also reproduce the issue by dragging nested Canvas from Hierarchy into Project window (making it into a prefab)
3. Reproducible in build of the project as well

Regression introduced in - 5.6.0f1
Reproducible with - 5.6.0f3, 5.6.0f1
Not reproducible with - 5.6.0b11, 5.5.2p3