One of the biggest misunderstandings when using pixelmator is that peopleexpect cropping to function on a layer. But in the Pixelmator world this is not possible. Cropping is always done on the whole canvas. In your video you actually crop your image twice. And when you crop the second time you think you crop the second layer, but you are actually cropping the canvas a second time and removing a part of the first image you imported.
So keep in mind that cropping crops the canvas, which means that everything, all layers and contents get cropped.
If you want to crop layers you should use the selection tool in stead. In the case of Pixelmator for iOS you can select the part you want to keep and copy it to a new layer. Then remove the original layer.
I've created a video tutorial that explains the Pixelmator philosophy when it comes to cropping and layers. - Cropping and Layers in Pixelmator