Little pests come silently: by end of day, crop is flattened (6-8)

'flattened' is the definition.
I don't know anything about this answer so I cannot tell whether this works.

'little pests come silently by end of day crop' is the wordplay.
I cannot quite see how this works, but
'little' could be 'l' (abbreviation) and 'l' is found in the answer.
'crop' could be 'craw' (synonyms) and 'craw' is located in the answer.
This explanation may well be incorrect...

'is' is the link.

Can you help me to learn more?