What about the investment in fuel, energy, water, and detergents: to collect the reusable containers, bring them to a sorting facility, sort them, bring them to the manufacturer, and wash them before they can be refilled?
Disposable containers are much lighter and cheaper since they don't need to be so durable for repeated washing and filling. The additional fuel costs of shipping heavier reusable containers around must be pretty substantial in itself, let alone all of the other steps.
And that's the problem in a nutshell: it's very easy to calculate the cost of mass-producing disposable packaging. It's much harder to calculate the cost of disposing of it (i.e. the impact on the environment).
Apparently the cost to use disposable packages, including disposing them after use, is lower than the cost of recycling for this particular chain. Most likely it is not really the cost of separating the containers into a separate bin or whatever, but the separate logistics train back to the manufacturer that costs more. The logistics to remove waste are there anyway, so if you can reuse that for packaging all the better.
While arguably the total costs including pollution are greater for disposable packaging, most of those costs are not borne by the corporation and so it makes sense (for the corporation) to skip using recyclable packaging unless there are other factors (for example, there are customers who will pay extra for the warm feeling of knowing they are helping to reduce waste).