When Daphne, Fred, and Shaggy run into each other in front of a clothing store, two mannequins clothed in the traditional Fred and Daphne apparel are visible in the store front.
Bugs Bunny and Yosemite Sam heads are seen covering golf club heads. These are characters from other properties owned by Warner Bros.
Shaggy and Velma were first romantically linked in Scooby-Doo! Mystery Incorporated (2010).
Although the gang presumably goes to the same high school as in Scooby-Doo! The Mystery Begins (2009), it's a completely different building. However, since we don't know how much time has passed between the two movies, it's possible that the old building was destroyed and a new one built.
The gang first encountered a giant frog creature in The New Scooby-Doo Movies: The Haunted Horseman in Hagglethorn Hall (1972). Here it's called a "lake monster", there it was called a "moat monster". A lake and a moat are both bodies of water.