Problem between files with same coordinate reference system

I have 2 shape-files. The first created with Qgis and the other with R studio(driver=ESRI). When I import them in qgis i see they doesn't "fit". Both have EPSG:4326 - WGS 84. The only difference I have noticed is that the second file from R studio doesn't have .qpj file. I know that whenever QGIS finds a .qpj file it will be used instead of the .prj (http://ift.tt/1Bq42FU). Is there someone who can help me to find if this file is the problem? What I get with EPSG:4326 - WGS 84 for both files is this: