From what I have been reading, both some of the Appeal Court judgement, transcripts of evidence being given to the public inquiry, and a podcast featuring an interview with Nick Wallis, the journalist who's been on the case for years, it seems that Fujitsu was a poor and struggling company when it was initially commissioned to develop this IT system. Witnesses have commented on the very poor quality of the software developers and incompetence in design.
It sounds to me as though the company was winging it for a long time, as protocols and procedures didn't seem to improve over the years. I wonder if the fact that they had a base in Tony Blair's constituency, which was threatened with closure should the contract be terminated, had anything to do with the decision to continue with Horizon, despite doubts about it, once the benefits payment element had been abandoned?
Wallis pointed out that Fujitsu has grown massively on the strength of that PO contract and is now a major UK government IT contractor. I only hope it's upped its game over the years.