In Season 1 Episode 5 (Deadweed), upon seeing the ghost miners coming back she says 'They're back...' in a similar way the ghost at the end of Disney's Haunted Mansions says 'Hurry back...'
The sounds the Shadow Clan make sound exactly like the Shadow Runners in another Nerd Corps show, Battle Force 5. Considering they're made by the same company, it's no surprise that they re-used sound effects.
In Season 2, Episode 3 (Inheritance), among the treasure that Will Shane had in his chest, there is an Aerrow Action Figure from another Nerd Corps show, Storm Hawks.
In Season 2 Episode 6 (Roboslugs) The Mecha battle between the Shane Gang and Quentin is a reference to the Mecha Genre in Anime.