Two entries for the same book - do you mean duplicate checking in calibre? You are better off with the Find Duplicates plugin for that.
As I mentioned above the metadata download process has some voodoo concerning ISBNs and Worldcat which mean I would never rely on the ISBN you end up with after metadata download having a particular significance. Perhaps with only a single metadata download plugin enabled that is not the case, I can't recall the code off the top of my head. But certainly with multiple download sources enabled there is no guarantees about what ISBN you will end up with.
There are a few other options, such as the Extract ISBN plugin. Or rather more manually the Goodreads Sync plugin, which via its "Linked Book" feature has the option of overwriting the ISBN to the specific edition you chose from Goodreads.
But duplicate checking via title/author with the Find Duplicates plugin is usually your best bet.