High fever but no infection

So we went to the doctor today as my 13 month old has had a runny congested nose for about 4 days and slight fever, which goes up at bed time but is ok by the morning and is slighty high during the day. When went to the doctor she said he had no infections and the temp then (3pm) was 37.1 but now at 18.45pm before bath time hes temp (rectual) was 39.1 ... I dont get it ... what could be the cuase if the doc didn't find any issue ...