You can use the multi-crop option to crop multiple pages at the same time while uploading a PDF or a file into the iOS app. This way you do not need to crop each page individually. This helps the app determine the borders especially when the page has columns, images, annotation, or page footer.
Here are the steps on how to do that:
Open the file you want to crop in the library.
Tap on the 'crop' option in the upper toolbar.
Tap on the 'crop' option (bottom left) after selecting the page, and drag sides to reshape the selected area.
Tap the '+' icon to create columns or the 'delete' option to delete the column
You can apply the same crop settings to multiple/all pages and tap 'Save'
Tap on the 'Thumbnails' to view the pages, after you are satisfied with your crop settings, tap 'Save & Listen'
Voila! You are done.