Welcome aboard to the Community, @yt96.
Let me share some clarification about receiving customer payments in QuickBooks Online.
Currently, the ability to make the Reference number field mandatory is unavailable. For now, I suggest editing the transaction in case a user forgot to enter the information.
We value your input about receiving payments from an invoice. I want you to know that we always make improvements in QuickBooks Online, and this preference might available soon.
While we assess, I suggest you visit our QuickBooks Blog to stay updated with all the changes with the product.
Also, I've attached some articles for a user to learn more about processing payments:
Feel free to drop a comment below if you have any other questions. I'll be more than happy to help. Wishing you a good one.