While cloning Linux VMs, two servers has the same MAC address. When SEP Linux Agent is installed on both of them and managed by the same SEPM, only one will report correctly.
Such behavior is expected, since SEP agents registers into the SEPM using a unique HardwareID, which is created based on the MAC address of the primary NIC.
Upgrade to SEP 14.3 RU8, where the HardwareID is a computation of the MAC address + UUID of the server.