Despite you see that the photos are there when you look with a file manager or on computer.

What happens is that the Media Storage service doesn’t properly index the photos/media. This is shown how it looks/works on a HTC One. This will force it to rescan, not all rescan apps works.

Go to Settings > Apps > All > Media Storage > Clear data and Clear Cache

Restart phone, and it can take several minutes (or many) for it to rescan everything. But, it should work. If it doesn’t: Do the same with Gallery (under Settings > Apps > All).