A typical element that won’t show up in Workshop but will appear as a dependency in Marketplace are “references to hardcoded object set, that are default values of variables in Workshop”.
To fix it, you need to backtrack which variables might have default values. An easy way that will always work is to delete half of the workshop, refresh marketplace, to see if the reference is gone or not. If not, bring it back, and delete the other half. Continue the dichotomy once you find which variable is affected.
Once you know which one has a default value, you can overwrite it by clicking on “set current value as default”: