It's pretty much an issue of the BOV/BPV not opening at the right time and/or at the right amount of opening.
Consider that the flutter occurs when the air charge hits a closed thottle plate, then slams into a compressor wheel, causing surge. This is a problem! Allowing the air an escape to recirculate until you get back on the throttle OR until the air is used up solves this problem. But, if you mis-tune the BPV/BOV, then the air won't release correctly or at the right time, causing some form of stall/surge. This is the flutter, and it is BAD on the turbo.
Sorry if that was remedial, but I was betting that some people didn't know what the hell it does.