New agent holds fifty in confusion (6)
I believe the answer is:
tangle
'confusion' is the definition.
(I know that tangle is a type of perplexity)
'new agent holds fifty' is the wordplay.
'new' is an anagram indicator.
'holds' means one lot of letters goes inside another.
'fifty' becomes 'l' (Roman numeral).
'agent' is an anagram of 'tange'.
'tange' placed around 'l' is 'TANGLE'.
'in' acts as a link.
(Other definitions for tangle that I've seen before include "Confused knot of something" , "At glen (anag.)" , "Get involved" , "A knotted mess" , "Twist together into a confusing mass" .)