Image Capture missing photos

I'm not sure which problems you want to avoid, but you could try this: Make an entirely new photo library; try importing using photos; if that works transfer them to your main photo library.

To make a new photo library you quit Photos; option click the Photos app, select create new, and name it something. Then, with Photos open, go to Preferences and choose Use as System Photo Library. That way, new photos will come into this new library.

If that works it won't mess up your normal library.

If you are using "optimise phone storage", that is what it will be. Any photos stored only in iCloud are not available for transfer to your mac. But in this case, you should be using iCloud to sync the photos to your mac, instead of a USB connection.