I have observed in the Space Plane Hanger the CoM does not behave properly. I suspect this is also the case in the VAB, but haven't done so much there in 1.11 yet, and would be less critical on rockets anyway.
1. If a part is translated, CoM appears to follow, but <space> resets the current offset translation back to where it started. CoM does not follow the reset until something else is done, at the very least turning the indicator off and back on.
2. Wherever the CoM is when the craft is finished, it will jump 1 standard offset click (like without <shift>) toward the