I was wondering if anyone could help me out with this - periodically when I select multiple CR2 files on Lightroom to "open as layers in Photoshop," it'll transfer all but one layer. I normally only notice this after I finish my edits (focus stacking) when I save/exit. The one file that was missing somehow immediately opens in Photoshop the same way you could click and drag a raw file into Photoshop with the Camera Raw interface. I hope this makes sense to read and thanks for helping!
Without exact system and version information nobody can really tell you much, including info on the actual camera model and things like metadata settings, fiel names, storage locations. This literally could be anything from PS ignoring the files due to botched metadata not matching the rest or trivial stuff like a hypersensitive input device inadvertently deselecting the files again while invoking the dialogs.