One of the biggest risks is, "nobody gives a fuck", which is why MVPs are so valuable. It lets you test market hypotheses.
But if you're building something handling real money, then a pretty obvious risk is, "The system will lose money beyond our capacity to absorb losses." Their failure to address that risk here is at best negligence.
But given the size of the loss, I don't think we should rule out fraud. The interesting question is, "When did they know they had a problem?" Sometimes shitty accounting systems are just naiveté. But when they persist over a long period of time in a way that just happens to cover up loss, embezzlement, or theft, then it's worth asking: did they keep the shitty accounting because better accounting would have forced them to admit something they were hoping to cover up?