Plot hole: Bonnie is the anchor for the other side and feels when supernatural beings die. How come she didn't know Katherine wasn't dead? Did she never think it was suspicious that she never felt Katherine's body after she died?
Other mistake: When Elena is taken, Bonnie asks Jeremy for help. She says she needs his blood to cast a location spell to find Elena. But it doesn't make sense. Earlier it was revealed that Elena is adopted, so she and Jeremy don't share the same bloodline and cast could not work well.