Hi there, Tracy117. 

I've seen you've exerted effort in explaining the situation of your client's issues in QuickBooks Online (QBO). And how you wish to determine the reason behind such an instance to stop it from happening.

QuickBooks tries to match downloaded transactions to any entries in your register automatically. You can review the matches before adding them to the register.

Also, QuickBooks makes a match if the bank feeds and the transactions that you've manually entered in the register have the same information (ex. check numbers, amounts, dates, and payees).

To ensure the matches are correct, I recommend creating banking rules. For more details, I suggest checking this article's Optional - Create rules to categorize transactions section: Add and Match Bank Feed Transactions.

I'd like to share this reference that you can check out to guide you in managing your bank transactions together with smooth reconciliation: Categorize and match online bank transactions in QuickBooks Online.

You can always find me here if you have any other questions about this or with QBO. I'll be around for you. Take care!