There is no sensible reason for a 100A C-curve MCB to resist tripping that a 125A D-curve MCB would respond to, short of one or the other being faulty (125/D too sensitive, 100/C not responding as it should).
I would suspect an unfortunate timing of faults behind this. Something downstream with medium/high MCBs and a fault would also trip a MCB upstream (but probably not a fuse, or a suitably configured MCCB) so you should check for that sort of thing.
Also Pete999 has a very important point - in a 3-phase system you really don't want to lose a phase if any loads are 3-phase (motors, etc) so you ought to be looking at linked 3-pole breakers.
Yes, you had 3 separate fuses before. But they ought to have been coordinated with downstream breakers so you get selective and so very little chance of a fuse going on a minor fault.
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Another though is the 125A D-curve had a poor connection and was heating up causing it to trip prematurely, and a change fixed that. But I suspect you would have seen signs of thermal stress there (or found it hot shortly after power off when replacing).