I was also having this problem, I managed to solve it by changing my package server.
In synaptic ->settings -> repositories
I had "Download from:" set to "Server for United Kingdom", changing this to "Main Server" and the issue disappeared. The dependencies for the epiphany-extensions package no longer includes a conflict for swfdec-mozilla so GNOME is again installable.
I was also having this problem, I managed to solve it by changing my package server.
In synaptic ->settings -> repositories
I had "Download from:" set to "Server for United Kingdom", changing this to "Main Server" and the issue disappeared. The dependencies for the epiphany-extensions package no longer includes a conflict for swfdec-mozilla so GNOME is again installable.