As far as we know, and this matches other bitcoin hacks, this is due to a straightforward information security issue, i.e. key compromise. MultiChain is similar to Bitcoin Core in that you have the option of keeping keys outside the node using whatever secure method you wish (including hardware devices or air gapped computers). You can build the unsigned transactions in MultiChain, then move them elsewhere for signing, then bring them back to MultiChain for rebroadcast. In a blockchain you can't really ask for more than that.
The other issue of course is that, being permissioned, a MultiChain blockchain doesn't have the same properties as the bitcoin blockchain in terms of the ability to irreversibly move a real bearer asset (bitcoin). In a permissioned blockchain, for each key holder, someone knows that key holder's real identity (otherwise it's not meaningfully permissioned), so any fraud can be tracked down and reversed. For example in MultiChain by default only whitelisted addresses are allowed to receive funds, so the fraudster cannot hide.