Yes, it's one pump for both circuits.
If the pump is unable to draw in water as fast as it is pumping it out, it will draw a partial vacuum. The pump is very powerful and the water will actually be forced to separate and leave little gaps of very low pressure "bubbles" suspended in the flow which create a lot of noise going through the pump.
This partial vacuum issue in a pump is called "cavitation", it will damage the pump if it is just ignored, it needs to be dealt with. The cavitation is not happening when brewing because the flow through the brew circuit is restricted by the gicleur, the coffee and everything else along the way, thus it isn't able to exceed the voulme that the pump is taking in. The boiler-fill plumbing is wide open when filling the boiler and the pump is trying to draw more than it is able to, possibly due to a restriction somewhere between the reservoir and the pump inlet.

Check a few things.
Is the reservoir pushed firmly, all the way down into position? If it is too high, the valve in the bottom isn't fully open.
If you push the reservoir downward during the boiler-fill cycle, does the noise get better?
Is the bottom of your reservoir nice and flat, or is it concave? When the reservoirs are taken from the blow-mold and sat upside down while they're still too hot, the bottom can sag due to gravity, the reservoir hardens like this, the valve in the bottom of the reservoir is too high to be fully held open by the shaft in the receiver (White cup) below it, and the partly open valve restricts the flow.
If not the above, can you hook up your braided hose to the plumb-in fitting under the back of the machine, switch the switch behind the reservoir to "Plumbed", put the free-end of the hose into the reservoir so that it has water to drink and test the boiler fill like that? If it doesn't make the cavitation noise when drawing from the plumbed in hose, then you've determined that the flow restriction is somewhere between the reservoir and the T-fitting where the 2 inlets join before the pump. There is also that little clear-plastic-inline-filter under the reservoir. If the above tests didn't locate the issue, you'll want to take the top off of the machine(Along with the reservoir carrier) and look to see if that clear filter is clogged with coffee grounds or anything.
If none of the above helps, post again. Hopefully the above will have ruled some things out.