Two economists have claimed that the ban in San Francisco led to an increase in food-borne diseases. The proposed mechanism is that people don't wash their reusable bags, and dangerous bacteria gets onto them. It isn't clear to me how strong the evidence for this is.
I’ve seen this also and have not seen any evidence to the contrary. Considering how damning this study is to plastic bag bans, I’m guessing this means there aren’t any studies that rebut these findings.
That’s one way to interpret the results. Alternatively, the study shows that in the normal course of human behavior, plastic bag bans may have nontrivial negative health impacts.
Also, it shows that in considering the carbon footprint of reusable bags, we should factor in regular (not occasional) cleaning.
Considering that a reusable bag needs to be reused many (hundreds, if memory serves) of times before reaching carbon neutrality versus single use plastic bags, this is not necessarily a trivial impact.
Carbon neutrality is not the only metric by which we create these regulations. Nor should it be. Single-use bags introduce many externalities that are captured and controlled by imposing a minimal cost.
Lots of stores also don't ask and give you a bag at whatever the locale's imposed fee is which they keep it, so there is an incentive to do this.
At the end of the day, the externality should not be captured by the store, but should be refunded back to the user with even distribution.