Ok, so I made some progress. I managed to get the hub/knuckle off but not before pulling my whole bloody driveshaft out of the diff, but thats another problem.
This is the BMW E90 rear hub / knuckle set up;
https://www.realoem.com/bmw/enUS/showparts?id=VB33-USA-08-2006-E90-BMW-330i&diagId=33_1230
And this is the hub / bearing;
https://www.realoem.com/bmw/enUS/showparts?id=VB33-USA-08-2006-E90-BMW-330i&diagId=33_1231
My question is, I managed to press the bearing into the knuckle and then I started to press the hub into the bearing (which was seated in the knuckle) and it was slightly off straight, so I stopped and when I took the hub out, it took the top of the bearing with it. Nothing seems wrong with the bearing, just appears to be a cover. It seats perfectly fine back on there and after pressing the hub in again (straight) everything seems smooth and quiet. I have a spare bearing (always buy 2 when you break things as often as I do) and wondering if I should swap them over?
Thanks guys.