Yes. Any deworming medication has the potential to cause side effects in your puppy or dog. Common side effects from tablets or liquids given to treat gastrointestinal worms include loss of appetite, vomiting, and diarrhea. Some medications, like Ivermectin, should not be administered to particular breeds of dogs. For instance collie breeds experience seizures, muscle twitching, and hypersalivation when treated with Ivermectin. Other deworming medications should not be given to pregnant or lactating dogs or puppies under certain ages. The safest and most effective deworming medications, or wormers, come from your vet or can be obtained with a prescription for your pooch.