The most common and most likely answer to this crossword clue is the 9 letter word DEMURRAGE
I've seen this crossword clue in The Times
D
E
M
U
R
R
A
G
E
More clues leading to the result DEMURRAGE
Buddy explains!

The straight part
We know that "penalty for lateness" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case penalty for lateness = demurrage.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 DEMURRAGE mean?
DEMURRAGE noun- (shipping) the detention of a ship or other freight vehicle, during delayed loading or unloading
- Compensation paid for such detention
- A charge made for exchanging currency for bullion