Recreation of problem:
A group with visible and hidden layers
Duplicate this group via CMD + J
In the new (duplicated) group, turn on one of the hidden layers
Invoke the transform handles for the group
The transform handles don't recognise the new size of the group with the incorporated hidden layer visibility. They only seem to transform the bounds of the original size of the group based on the visible layers before duplication.
See the video for more clarity:
https://www.loom.com/share/dc106a51978a42abbf56c7e718de3647