May be I am echoing Mr Prasad's comments, or may be not.Geeta explains well...give it a read again.
Let me try giving my opinion here(unproven opinion)..
Water...at the molecular level its H20 .
Now the H20 molecule resides in the human body, in plants, in animals, in clouds etc.
All of them house H20 molecules.
H20 is in all of them but they are not in H20 and neither is the human body/plants/animals/clouds H20.
Just replace H20 with Brahman in my above example.
I hope I made some sense.
My understanding: Brahman is said to be cause of everything. In the example given, water is very different from the plants, human body, and animals etc. Water is NOT the cause of all those bodies and hence it can be in each of these bodies.
So while the example is clear how does it apply to explanation about Brahman?
Also Gita verse 9.4 and 9.5 say exactly the opposite LOL