Typically the CL fuses in a VFD that is part of an MCC are only there as current limiters when the AIC rating of the bucket needs to match higher levels than the VFD has been tested for. They are not generally intended to be part of the coordination in that their only purpose is to limit fault energy to a level that the other devices can withstand in case the upstream devices fail to clear it. So to avoid having those fuses clear in a nuisance fashion, they are oversized for the circuit.
What I find odd is that all three SCPDs were cleared. Usually if it's a coordination study problem the wrong one clears first, but once the first one clears, why would the others clear too? The only thing I can think of would be that the diode bridge rectifier suffered a massive failure and shorted all three phases, bolted fault or ground at the same instant and something l;ike 65,000A tried to go through. The fuses then cleared because the upstream breakers were taking too long, but they had already started their process of tripping, so they just continued even as the fuses were clearing. The down stream breaker should have cleared first, so that's still a coordination problem of course, I'm just theorizing on why you would have blown fuses AND two tripped breakers.
Must have been one heck of a failure.