If your images are showing as unified files like in the screenshot below and images are missing from your second camera, it's highly likely that the name of your files are the same:
You can resolve this through the following steps:
1. Open your project in Select > Right click on one of the images and click on Show in Finder
2. Inside that folder > Create a CR2 subfolder and CR3 subfolder
3. Filter the CR2's and move them to that subfolder
4. Do the same with the CR3 files
5. Once that's ready, go back to Select > Refresh the Gallery
You should now be able to see your CR2 and CR3 images separately.