When I release the clutch at 3:rd or 4:th gear on my -98 BMW 328i, it makes a little low pitched squeal, for maybe half a second. This is not an issue on the other gears however.
What could be at fault?
I would imagine it is the clutch throw-out bearing (alternately called a release bearing). When the clutch pedal is pressed the bearing starts rotating inside the housing. When the clutch pedal is released the bearing stops rotating in a second or two once the pressure is removed from it. Normally, it's silent but bearings can make squealing, grinding, coarse noises when they start wearing out.
You can see it in the picture below (it's the blue thing)
The downside is that replacing it means digging into the transmission, which means replacing the clutch, too. I have worked on my E46 enough to know that this would be... um... less than fun, and would require special tools that you very well may not have. I'm reluctant to guess what a shop might charge.
Maybe it's worth waiting until the clutch needs replacing before doing anything else.
I hope that helps.