The backtrace suggests a fd leak but it could be another process having
the issue and just letting the system in a state where gdm errors out
due to it

Could you use lsof to figure out what process is using the fds?

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  gdm3 crashed with signal 5 in g_wakeup_new() from g_main_context_new()
  from g_dbus_connection_send_message_with_reply_sync()

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