It depends a lot on the company, and maturity level of its management. I believe that the most challenging problem is actually to understand the business context (strategy) that stands behind a KPI. This article explains some typical pitfalls and shows how to avoid them.
Also, another typical challenge is that companies often use spreadsheets (like MS Excel) to keep their KPIs. That’s fine for a prototype stage, but when you need to build a strategy map and align your KPIs with that strategy map (the business context that I mentioned above), then one needs to have a good software for scorecards, like for example BSC Designer.
What are some difficulties that the company will face when generating the KPI?