Apple Photos uses a media library for the photos, which Excire unfortunately cannot access.
To get them out of Apple Photos, you need to export the images from there to disk (using the export feature in Apple Photos). From there, you can add the folder with those images into Excire Foto.
In the future, if you want to transfer photos from the iPhone directly to the hard drive (without going through Apple Photos), you can use the "Image Capture" app in macOS to do this.