The intranasal bordatella vaccine can cause the very disease that you are vaccinating against. It is said to be less severe (hopefully). A lot of of people decide not to give it because of this and because it is non-core.
If your pup has been coughing and isn't getting better, you probably need to see a vet. I would guess this reaction had nothing to do with the lepto vaccine. However, the lepto should only be given in certain areas of the country where the dog is at very high risk or never at all. It should not be given just because the vet has a combo shot there that they feel like using...
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