I found this on the web.

"Although dog and cat manure both contain organic nutrients useful to plants, neither is safe to use in soil containing food crops. Both contain parasitic pathogens that are harmful to human health. Dog manure can contain the eggs of Toxocara canis (the common large roundworm), which can also infect humans. It's estimated that 90% of young puppies are infected with this worm-many are born infected-and up to 50% of all adult dogs. The eggs can be transferred to the human mouth by a person's fingers or from foods that have been in contact with dog feces. Toxocara eggs can remain viable in the soil for up to 10 years depending on environmental conditions. Because no information is known on the effects hot composting has on Toxocara eggs, it also unsafe to add dog manure to compost heaps intended for food crops. If you have a dog feces problem in your garden, remove the feces and take care to use good hygiene practices (thoroughly washing hands and vegetables) to avoid possible contamination."

Also, google a search on "dog poop/feces garden." A gardenweb search will find opinions as well. eg...Kelly Slocum from the vermicomposting forum advises strongly against using/allowing dog feces in the garden.

Make certain you clean up your garden of all the feces you can find, with disposable gloves, bag it and throw it away.
Readers Digest did a story on cat feces long ago in how sometimes their feces has a grub in it that if humans eat it will get into the brain. The story was about a child in a sandbox playing where cats had used it as a toilet.
There is an old rule for health, if it eats meat do not use it in the garden. That is one reason vacationers are warned as are soldiers to not eat uncooked foods in certain nations as they use raw human waste for fertilizer.
It is a broad subject, but no you have not messed up the chemistry in your garden, but puppies should be thought of as having worms until wormed by a vet.
Make sure you wash your garden produce that comes out of the ground this year too please.

Make sure that it is not parvo virus. Bird in your backyard can spread parvo virus so you must be careful.

Here is a link that might be useful: symptoms of dog poisoning

Is this a food garden or a flower garden?
It wouldn't worry me at all unless youw ere growing root crops.
but to avoid the unplesantness of digging in dog poo, I would dig a hole about a foot or more deep and about a foot wide and put the waste in there....when it's almost full, cover it up and dig another hole....after about a year that doggid doo doo will be well composted and broken down by soil organisms.
BUT if your dog has hookworm I would flush the feces down the toilet until you are sure all eggs have been eliminated.
Linda C