Hi,
I think, you should wait for a day or two and continue with the doctor's prescription. It is no surprise that kids cry because of cold as their nose gets blocked and since they are so small they get irritable switching into breathing from mouth. I say this because my daughter often cries at night when her nose is blocked or have congestion. She cries off and on because her sleep is disturbed because of disturbance in breathing. I suggest wait for a day or so and if she still doesn't show any improvement, visit the doctor again.
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Dada of 1 lovely daughter