Hello,
the APK:CloudRep [Susp] is a warning-like message for applications that are very new/rare/previously unseen in our userbase.
There are various reasons as to why one of the apps is detected and the other is not, the most probable of which is, that the first one has already been installed on a few devices previously, other reasons may include that it has been installed from a trusted source - like Google Play or similar or that the app is signed with a trusted certificate.
It is hard to tell the exact reason for the warning showing only on the one app if we do not have the samples at hand or at least their sha256.
Also if you are a developer, there is an option to disable these reputation-based services in the 'App shield' for AMS4 and 'Settings -> Real-time protection' in the new AMS5.
I hope this answers your question.
Best regards,
Ondrej