Line’s included in church hymn: we must think it’s a bloomer! (13)
I believe the answer is:
chrysanthemum
'a bloomer' is the definition.
(chrysanthemum is a kind of flowering plant)
'line's included in church hymn we must think' is the wordplay.
'line's' becomes 'ry's' (abbreviation for railway).
'included in' means one lot of letters goes inside another.
'church' becomes 'ch' (abbreviation on maps etc).
'hymn' becomes 'anthem' (synonyms).
'we must think' becomes 'um' (hesitation).
'ch'+'anthem'='chanthem'
'rys' going inside 'chanthem' is 'chrysanthem'.
'chrysanthem'+'um'='CHRYSANTHEMUM'
'it's' is the link.
(Other definitions for chrysanthemum that I've seen before include "Ornamental plant" , "Flower depicted on Japanese Imperial flag" , "Ornamental flower" , "National flower of Japan" , "Common garden plant" .)