If it was separation anxiety it would be there all the time, no matter who put your DS to bed.
Children can easily tell if one parent will 'give in' easily and give them what they want - ie to sleep in Mum and Dads bed.
We have similar with all our children, but the other way around. If our (older) children wake in the night and walk into our room - they always go to DH side of the bed. Why? Because DH opens the duvet and lets them get in. Then complains and gets very grumpy about it in the morning. Whereas if they come to my side of the bed, they know I will instantly turn them around and walk them back to their own bed.
DGH grumbles, why is it always him who has the disturbed night with children on his side of the bed. Why can't they go on my side for a change. He knows full well why.
I could give a similar example with whining. Child asks dad something, he says no, they whine and winge and keep going on and on about it - until he gives in and gives them whatever it is. They come to Mum and ask the same thing, I say no. They ask again they get told off and sent to their room.
DH asks why he gets all the whining yet the children immediately accept no from me. I don't ever give in 