It protects new snake and duck having trouble (2,1,4)
I believe the answer is:
in a spot
'having trouble' is the definition.
(I've seen this before)
'it protects new snake and duck' is the wordplay.
'protects' means one lot of letters goes inside another (outer letters protect inside letters).
'new' becomes 'n' (common abbreviation eg NT for New Testament).
'snake' becomes 'asp' (asp is a kind of snake).
'and' means one lot of letters go next to another.
'duck' becomes 'o' (resembles zero - 'duck' in cricket).
'n'+'asp'+'o'='naspo'
'it' going around 'naspo' is 'IN A SPOT'.
(Other definitions for in a spot that I've seen before include "Awkwardly situated (colloq.)" , "Facing difficulties" , "Badly placed" , "Having trouble" , "up the creek" .)