Problem With Lenovo A6000 - Inbuilt Malware

I have a Lenovo A6000 Plus, there are some strange softwares that 360 antivirus app detect as Malware and indeed are malware. Because the phone has two Android System app one with proper Android system logo and another with generic android app logo.

These app open automatically and are shown in the recent app, even after closing it everytime they populate the recent apps again and again.
I have factory reset the phone multiple times. Still have that problem.

Here is a screenshot: