Punishes for the broken pane and the silly lies, the son (9)
I believe the answer is:
'punishes' is the definition.
(I've seen this before)
'broken pane and the silly lies the son' is the wordplay.
'broken' is an anagram indicator.
'and' means one lot of letters go next to another.
'the silly' indicates an anagram.
'the son' becomes 's' (genealogical abbreviation for son).
'pane' with letters rearranged gives 'pena'.
'lies' is an anagram of 'lise'.
'for the' is the link.
(Another definition for penalises that I've seen is " Punishes".)