For example, there's a package A (1.0.0) that depends on packages B (1.0.0), C (1.0.0). If package A is updated to version 2.0.0 that depends on B and C versions 2.0.0, packages B and C would still be listed as having version 1.0.0 in the "manifest.json" file.

How to reproduce:
1. Create a new project (using the default 3D template)
2. Import an older version of a Package that has dependencies (i.e., Entities)
3. Update one of the dependencies or add it to the manifest.json file (so it would be listed, i.e., Jobs)
4. Inspect the versions listed in the "manifest.json" file and the Package Manager
5. Update the main Package
6. Inspect the updated dependency version in the Package Manager
7. Compare it to the "manifest.json" file version

Expected result: Dependency's version listed in the Package Manager and the manifest.json is the same
Actual result: manifest.json has the older version of the package even though it's updated in the Package Manager

Reproducible with: 2019.4.20f1, 2020.2.5f1, 2021.1.0b7, 2021.2.0a6
Couldn't test with: 2018.4.32f1 (Dependent packages don't change the version in the Package Manager nor in the manifest.json and package dependencies are not listed)