Not all of the transactions from the bank are migrating over to quickbooks, how do I fix this?

Welcome to the Community, @erskineconcepts.

I'll share information about bank transaction importing issues.

Let's perform troubleshooting steps for this concern.

Additionally, it would be helpful if you could let us know which exact bank you use so that we can find out whether there is a problem with the bank currently.

Let's perform a manual update to refresh the connection between your bank and QuickBooks Online in the interim.

Here's how:

• Go to Banking from the left menu.
• Select the Update button in the upper right.
• Select Update Now.

Then, you can categorize and match transactions in QuickBooks online to avoid messing up your books. Check this article for reference: Categorize and match online bank transactions in QuickBooks Online.

Let me know if you have questions about missing bank transactions. I'm always here to help. Have a great day.

@erskineconcepts 

You can use MT Online or one of converter tools (e.g csv2qbo) as a workaround.

https://www.moneythumb.com/?ref=110