Yes, it can be confusing (and sometimes funny).
'hati'= liver, but only in a medical/anatomical sense.
(if you're a doctor performing surgery or if you're eating chicken liver).
'jantung' = heart (in a medical/anatomical sense).
'jantung' is not 'heart' in a romantical way.
It's the organ that keeps your blood pumping.
It is quite common across languages. In Mesopotamia the liver was thought to be the organ of thinking, making of similar importance to the heart.