If they are use once tokens then you need to get more. If implemented badly, they could be asking for a new one every time, and now the issuer knows whenever you are using them. I'm not sure exactly what implementstion flaws The EFF article was talking about but they have links if you want to learn more.
Edit: also, now that I think of it, if it's single use, then they need to be invalidated every time they are used. So this probably also notifies the issuer every time a token is used, and which token it was. There are probably ways to do this privately but it is a tricky problem, and something the government probably won't get right the first time, which is the main issue that the EFF is talking about.