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I've found three gnomes. One was in the City of the Dead, but I couldn't find a way to get to it. I didn't even know what it was, I could just see something weird floating behind a statue next to a chest, but after collecting two others I realise now that it was a gnome.
The second one I've seen was in the Ivory Citadel, after cleansing the second water spring, I had remembered seeing a small offshoot tunnel blocked by a large pool of corrupted water, so I decided to go check it out. There was a Gnome, the first one I actually collected.
The third one was in Black Stone. There was one section, not long before the boss fight, where you had to go back in time to shatter some crystals, return to the present to get the key, then go back in time again to use the key on the locked door. The gnome is in the corridor behind the locked door in the present time. So you had to go through that corridor in the past, then use one of the time portals on the other side to return to the present, then backtrack back through to that corridor. The door that was locked is still locked and sealed in the present time, but the gnome is right there.