QB Issue Resolution:

When you create an invoice with a class and make a deposit without the tracking, the calculation of your transactions will not affect it.  However, when you customize the report to Class the deposit transactions will show as unclassified.

I attached a screenshot for your reference.

You may also check this article to learn more about Class tracking: How to Use Class Tracking in QuickBooks.

Resolution for Issue 'Class tracking. If I have a class on my invoice but then when I make the deposit I don’t put a class, how does that effect my reporting?' available: Yes (Solved).
Source: Intuit Community forum.

Class tracking. If I have a class on my invoice but then when I make the deposit I don’t put a class, how does that effect my reporting?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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