Problem that is small with precious stones? (6)
I believe the answer is:
rubies
'precious stones?' is the definition.
(ruby is a kind of precious stone)
'problem that is small' is the wordplay.
'problem' becomes 'rub' ('there's the rub').
'that is' becomes 'ie' (abbreviation for id est, 'that is' in Latin).
'small' becomes 's' (abbreviation - e.g. clothes size).
'rub'+'ie'+'s'='RUBIES'
'with' is the link.
(Other definitions for rubies that I've seen before include "Red gemstones" , "Deep red jewels" , "The Stones in the red" , "Deep red gems" .)