I agree, it seems like if you set preferredContentMode to desktop, then the User Agent should probably be "desktop".
However, WKWebView has a customUserAgent property, so you can just use some string manipulation to "fix it".
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So, more specifically: you need to see the logs for a WKWebView in an app that is not yours. Sounds very challenging!
We are having the same problem. It may be related to the application holding the web view going into the background / becoming inactive, but not clear yet.
We've wrapped our indexedDB calls with retries which helps in some cases, but they still more often just retry a few times and eventually fail with the same error. Would be interested to hear if you have made any discoveries or progress.