Perhaps a jealous beetle. If there's something valuable in Bugtown, like a special type of pollen that gives bugs superpowers or something, a beetle might be envious of those who have access to it and try to disrupt things. He could be spreading false rumors or causing little accidents to throw the town into chaos.
Another possibility is a group of outsider bugs. They come from a different part of the forest and don't understand the ways of Bugtown. They might accidentally be causing trouble because they are so different. For example, they could be using up all the water sources or trampling on the little bug gardens without realizing they are doing something wrong.
I haven't actually read the 'Mystery in Bugtown' story, so I can't give a detailed summary. But generally, in a mystery story set in a town like Bugtown, there would likely be some sort of strange event or disappearance. There could be a cast of interesting insect - like characters. Maybe a valuable nectar has gone missing from the main flower in town and all the bugs are suspects.
It could be an evil wizard who wants to use Sonic's speed and Amy's strong will for his own dark purposes.
It could be an evil toy - maker. He might have created the Lalaloopsy dolls with a dark purpose in the first place. Maybe he wants to use their magic for his own evil gains and has now come back to take over the Lalaloopsy world.
Cinderella herself could be the villain. In a dark take, she might be using her charm and the situation to her advantage in a malicious way. For instance, she could be faking her kindness to the prince just to get into the palace and then cause chaos.
A rogue ninja from another village who is jealous of Ino's talents and the reputation of her village could be the villain. This ninja might think that by kidnapping Ino, they can bring down the morale of her village and prove their own superiority.
Ares could be the villain in this story. Since Wonder Woman is without her belt, Ares might think she is weakened. He could try to take advantage of this situation to spread chaos and war. He may have a new plan to finally defeat Wonder Woman once and for all, seeing her without the belt as a sign of vulnerability. Moreover, Ares could be using some new minions or powers that are specifically designed to counter a beltless Wonder Woman.
In a reverse little mermaid story, the mermaid herself could be the villain. Instead of being the kind - hearted character we know, she could be cruel and use her charm to manipulate humans for her own gain.
Mojo Jojo is a likely villain. He's always trying to outwit the Powerpuff Girls, and hypnosis could be his new devious plan.
Maybe a disgruntled former elf who was banished from Santa's workshop. This ex - elf holds a grudge and uses a dark magic spell to shrink an innocent elf, hoping to create chaos in the Christmas operations. He thinks that by doing this, Santa will be so distracted that he won't be able to deliver presents on time.
A corrupt politician could be the new villain. He uses his power and influence to cover up his illegal activities, like embezzling funds meant for the city's development. The Punisher would see through his lies and decide to take him down.