The light ones likely have thinner necks. If thats the case, consider culling those cases. There's no fix except for neck turning the fat(normal) sized cases to match them. Something else to note is that those bushings are not perfect. Despite their markings, they may be smaller or larger. If you're not using an expander ball, you can take some micrometer measurements of the sized neck to give you an idea of what it's actual size is. Dont forget that the necks are springing back some after sizing. I have some redding bushings that are .001-.0015 undersized. When you move between your .288 and .289, you could be seeing some of that. They are generally tapered somewhat as well. If you flip that .289 over (run it numbers down), you'll probably get a little more sizing. The exact amount varies from bushing to bushing. Fwiw, I run wilson bushings when i can. I own dozens of bushings, and the wilsons are more consistent, have better internal finish, and better tapers.
Do you anneal? Is it possible you overcooked some of the necks?