Why are there 2 instances of each app on my phone?
This seems to be dual app feature of Lenovo and some Xiaomi phones

This enables dual SIM phones to run two instances of an app say WhatsApp and the second instance has an icon as described in the question

You need to go to settings and disable that - Settings &rarr; Feature &rarr; Dual App Profile (this may not be the exact path depending on OS version but search in settings for dual app)