Graduate makes a case, penning short excuse (9)
I believe the answer is:
calibrate
'graduate' is the definition.
(I know that graduate can be written as calibrate)
'a case penning short excuse' is the wordplay.
'a case' becomes 'crate' (both can mean a container).
'penning' is an insertion indicator.
'short' means to remove the last letter.
'excuse' becomes 'alibi' (excuse given by a suspect in an investigation).
'alibi' with its last letter taken away is 'alib'.
'crate' enclosing 'alib' is 'CALIBRATE'.
'makes' acts as a link.
(Other definitions for calibrate that I've seen before include "Fine-tune an instrument" , "Mark positions" , "Mark (a gauge) with a scale of readings" , "Adjust (gauge for accuracy)" , "Correlate instrument readings with a standard to check accuracy" .)