An example from my field: in financial modeling the typical pattern is to calculate an initial cash flow followed by further projected cash flows at fixed intervals (e.g., monthly). The natural way to store a series of cash flows (besides as a column in Excel) is just as an array, and if that array is 0-indexed, the index represents each cash flow's offset from the initial cash flow. This is both more natural and more convenient for lots of calculations - e.g., when calculating the net present value the number of discounting periods for each cash flow is just its index in the array.
I haven't encountered a code base that uses non-default array indices, but it sounds like a serious anti-pattern, especially if you're just changing from 1-based to 0-based.