That's a good question, auhyrek. I know a few things that cause the downloaded transactions to be missing.
There are times when a transaction may seem to be missing when it's just been mismatched. You can go back to the downloaded transactions, and see if they were matched correctly. Another reason is having incorrect filters on your Bank Register. To check the filters, simply follow these steps:
Click Accounting on the left panel.
Select Chart of Accounts.
Select the bank account from with missing transactions.
From the Action column, click View register (or Account history).
Sort the register by the entries in the Date column.
Select the Filter icon, above the Date column.
From the Reconcile Status drop-down menu, choose All.
Select Apply.
Additionally, you may want to refer to the following before you download:
Some banks and credit card companies don't post transactions for download until later in the day or the next morning.
Some banks will show a transaction on their website but won't download the transaction until it posts.
If the missing transactions are the most recent ones, wait at least 24 hours in case your bank doesn't make them available immediately.
You can also do a manual update to ensure that you have the most current view of your bank's data. For the complete steps and details about missing transactions, you can refer to this article: Bank transactions are duplicates, missing or wrong or bank balance not updating. Just scroll down and proceed to the Missing transactions section.
I'll be right here if you have more questions.