I am running Wix 3.11.1 and when trying to do an upgrade the upgrade goes into maintenance mode and leaves two entries in Add/Remove programs list.
A short version
The log shows the upgrade was successful, installing the new product and removing the old one. The most likely explanation for the two entries in Programs&Features is that there is one for the actual MSI product and another from the WiX bootstrapper. You probably need to suppress the MSI one with ARPSYSTEMCOMPONENT=1 or with WiX bootstrapper support for suppressing the MSI's entry.