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.
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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!
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".