Reproduction steps:
1. Create a new Unity project.
2. Go to "Window > Lighting > Scene" and uncheck "Auto" checkbox.
3. Save the scene.
4. Create a reflection probe and click "Bake" in the inspector window.
5. Create another reflection probe and click "Bake" in the inspector window.
6. Go to "Assets > [SceneName]" in the project window.
7. Click on the "ReflectionProbe-0.exr" with the right mouse button and select "Find References In Scene".
8. Notice, that both reflection probes reference the same texture(GIF attached).

Workaround:

• Go to "Window > Lighting > Scene" and click "Build" or reopen the scene and bake each reflection probe manually again.