Firstly you should always check that you are comparing like with like data.
For example if you are looking at the data in Xero/QuickBooks that has been sent from Link My Books and comparing it say your business reports from Amazon then it's not likely to match up.
Have a look at this help article to understand the reasons for this. Although this help article relates to Amazon, the guidance in here would apply to other sales channels too.
Have all your settlements been sent to either Xero or Quickbooks. Check your Link My Books settlement dashboard and ensure they have the Status 'Sent'
Have any of your settlements been sent more than once or have they been voided/deleted? Check out 'Voided or duplicated settlement invoices/journals in Xero/QuickBooks' for further information
If you use Xero do you have any invoices waiting to be approved? Check your invoice list. To ensure your invoices are approved when they send to Xero, check Settlement Settings in Link My Books.
Have you correctly matched your bank deposits with your invoices/journals?
For further help please look at this help article 'Unable to Reconcile in Xero/QuickBooks'