The most common and most likely answer to this crossword clue is the 9 letter word FOUR-PACK
I've seen this crossword clue in The Guardian
F
O
U
R
-
P
A
C
K
Buddy explains!
The straight part
We know that "two items less than perfect order, stomach-wise" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case two items less than perfect order, stomach-wise = four-pack.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.