I tried to reproduce the issue on my side, unfortunately with no success. Executing the same test of yours resulted with correctly returned collection. I have shown this in the attached Screenshot1.png.
To be able to continue investigating the issue on my side, I will require a sample project that can reproduce it. Please, if it is possible send me such project with your next message.
Another thing you can try is to drop the MockBatchManager class and directly arrange expectations to the BatchManager class. Then, to execute the protected method you can use the PrivateAccessor coming with JustMock. I have prepared an example that should give you more detailed explanation:
public void AddOrUpdateLoadCarrierRequestAddsAnElementToEveryDictionaryWithPrivateAccessor()