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As far as I understand you layout you have packages in two repos A and B. And some from A depend on some in B as well as some in B depend on some in A. That is a circular dependency and is not a supported layout with the ROS tools. For releasing with bloom it is a chicken-egg-problem since neither can be released first since its dependencies are unavailable and therefore no Debian control files can be generated.
So you shouldn't expect this to become supported anytime in the future but consider to refactor the separation of the packages into repos in way which is not circular.
To work around the issue you can do the following process (which will take significant extra effort): * release the packages from repo A while blacklisting all packages which have dependencies from B * release the packages from repo B (hopefully the released packages from A cover all dependencies, otherwise you need to to the first two steps repeatedly adding more packages every release) * then release repo A again but without blacklisting any packages.
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