Often what counts as rational is not nearly as clear as it appears; there are lots of load-bearing things hidden in the noise and "irrationality" that actually matter in practice.
For example, for capturing indirect effects or time-series effects.
Another example: if you're playing a one-off game, defecting is often the "rational" move.
But one-off games are extremely rare in the real world; you'll often have repeated games, with the same, or indirectly overlapping, counterparties.
In those cases, defecting is not rational, even though the situation seems similar!