Dependencies are added twice with different versions when I try to update a dependency version

**Environment**:

- *Jib version:* 3.3.1
- *Build tool:* jib-gradle-plugin:3.3.1
- *OS:* ubuntu/docker-container

**Description of the issue**: When I update a dependency (for example due to a security vulnerability), jib added the old and the new versions of the same dependency to the container. This also leads to failing of container-scanner stage in my pipeline, since the old vulnerable dependency still in the container.

**Expected behavior**: Only the new version of the dependency should be in the container.