An amphibian caught rising pong; that’s a shame! (3,3)
I believe the answer is:
too bad
'that's a shame' is the definition.
(I've seen this in another clue)
'an amphibian caught rising pong' is the wordplay.
'an amphibian' becomes 'toad' (toad is a kind of amphibian).
'caught' indicates putting letters inside.
'rising' says the letters should be written in reverse (going up in a down clue).
'pong' becomes 'BO' (body odour).
'bo' in reverse letter order is 'ob'.
'toad' going around 'ob' is 'TOO BAD'.
(Other definitions for too bad that I've seen before include "Informally regrettable - excessively wicked" , "I have no sympathy" , "Informally regrettable, a pity" , "What a pity, hard luck" , "regrettably" .)