'ada' = there is (presence).
'ada yang' = there is something that.
'ada yang memisahkan kalian.' = there is something that separates you.

'jangan' is a negation used in imperatives.

'Jangan ada yang memisahkan kalian.' = Don't let there be something that separates you.
'Jangan ada yang memisahkan kalian.' = Don't let anything separate you.