First, you should report this issue to Esri support. They will need full details and more than likely a copy of your database.
If you have two tiers in your network, Transmission and Distribution, and you enable the topology and then run update subnetwork in the distribution tier first, then try to run update in the Transmission tier on a subnetwork, you could encounter this error. You could also encounter in the same tier if the first subnetwork processed has a very small extent. You should try starting with running update subnetwork with the subnetwork that probably has the largest extent.
But again, please submit an issue to Esri support.
John Alsup
jalsup@esri.com