The most common and most likely answer to this crossword clue is the 6 letter word CRATES
I've seen this crossword clue in The Times
C
R
A
T
E
S
More clues leading to the result CRATES
Buddy explains!

The straight part
We know that "boxes" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case boxes = crates.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.
What does CRATES mean?
CRATES noun- A large open box or basket, used especially to transport fragile goods.
- (mildly) A vehicle (car, aircraft, spacecraft, etc.) seen as unreliable.
- In the Rust programming language, a binary or library.
- To put into a crate.
- To keep in a crate.