Artie refers to the "near catastrophe in Yosemite" when explaining what was done to H. G. The incident with the trident happened in Yellowstone.
At the very beginning, as agents search for the source of a disturbance and Myka says "The archive is safe," the statue of Zeus can be seen behind her, even though it was moved off-site in "The New Guy."
H.G. Wells's hair is moved by the breeze, despite being a hologram.
When Myka conveys to Pete her discoveries in Emily's apartment, she's far too loud about it. Her voice would easily carry through the archway into the next room for Emily to hear.