Hi Khayam,
Thanks for reaching out, I’m James, one of the Support Engineers here at FreeAgent 
This may be a result of the way all our API endpoints default to a standard pagination of 25 items per page. A more in depth explanation can be found here.
You could try something like:
https://api.freeagent.com/v2/credit_note_reconciliations?page=1&per_page=100
This will get get the first 100 and potentially if you have more you can update the page value to cycle through the pages.
Please let me know if this doesn’t solve the issue for you and I can take a further look.
Many thanks,
James