probably because the parenthesis have an unbalanced nested parenthesis

Having unbalanced nested parenthesis invalidates your question. You asked for the following:

input: '(aaa) (bbb (ccc( ddd) eee) (fff)'
output:
   '(aaa)'
   '(bbb (ccc( ddd) eee)'
   '(fff)'
[download]

but the unbalancing could have been resolved as in imp's answer, or alternatively as follows:

input: '(aaa) (bbb (ccc( ddd) eee) (fff)'
output:
   '(aaa)'
   '(bbb'
   '(ccc( ddd) eee)'
   '(fff)'
[download]

As a matter of fact, I would understand either taking them all like imp (i.e. assuming that the missing parenthesis are all in the end) or this last one (i.e. assuming that the missing parentheses close the littlest possible group), while I don't see a generalisation rule for your choice.