The coughing and wheezing could very well be kennel cough and it was likely caused by the bordatella vaccine (drops in her nose). This is what the vaccine is supposed to prevent but sometimes it causes it.
If it is kennel cough, they can get pneumonia secondary to it, so I'd watch her close.
Lethargy is common after vaccines.
She should be back to normal within about two days after.
Was the lepto vaccine given?
This causes it in particular and can be very dangerous to small dogs.
With the vomiting and diarrhea, make sure that she isn't dehydrating.
If she is very small and still isn't eating, an IV at the vet may need to be considered.