mongobee has incompatibilities starting with version 4.2 of MongoDB, and versions of the Mongo Java driver starting with version 4. Specifically, mongobee uses the system.indexes collection, which was removed in MongoDB 4.2 (mongobee#104). It also uses version 3 of the Mongo Java libraries, which is incompatible with changes made in version 4 of those libraries (mongobee#115). Additionally, by all appearances, mongobee has been abandoned since 2018.
Removal of system.indexes and system.namespaces Collections
Starting in version 4.2, MongoDB removes the system.indexes and system.namespaces collections (deprecated since v3.0).
What's new in 4.0
This release adds no new features but, as a major release, contains breaking changes that may affect your application. Please consult the
Upgrading Guide for an enumeration of the breaking changes.
Mongock, on the other hand, is actively maintained and supports the newest MongoDB versions and Java libraries.
Mongock is therefore going to be the better choice of libraries in virtually all practical situations.