I got two different number of items in a merged or dissolved layer

I’m using QGIS and I have the locations toxic waste sites in the U.S. on my map. I also have the weather warnings as a polygon on my map. I want the number and list of toxic waste sites in those polygons. The first time, I merged the weather warnings into one file, and clipped the toxic waste sites in the area of weather warnings, with the toxic waste sites as the input layer and the merged weather warning polygon file as the overlay. The second time, I dissolved the weather warning polygon, and did "count points in polygon." I’m getting different numbers. Is there a reason why this is happening?