If the issue is with including transitive dependencies that are in your own codebase, then you should annotate the public interface header to the implementation details with IWYU Pragmas [1] that export the implementation (for example [2]).

If this is in third-party libraries, you can use IWYU Mappings [3] to map the "private" headers (usually the transitive include) to the public interface. An example that I use for the PEGTL library [4].

[1]: https://github.com/include-what-you-use/include-what-you-use...

[2]: https://github.com/anand-bala/signal-temporal-logic/blob/800...

[3]: https://github.com/include-what-you-use/include-what-you-use...

[4]: https://github.com/anand-bala/signal-temporal-logic/blob/800...