I haven't seen that myself... we had only started putting Apple Pay on our sites, then we migrated and don't have that re-implemented yet (we may never, as I recall it was painful and we didn't seem to get a lot of interest)... and the Apple Store payments through our iOS app would be a completely different flow, so not really comparable.
Does your Apple Pay implementation auto-send users back to your site to a dedicated thank you page on your site? It seems unusual that someone would exit out of the payment flow until they had a proper payment confirmation screen....
How far off are your numbers? Could the difference be due to opt-outs on tracking or active analytics blocking? Have you been able to replicate the issue in test mode on your dev/qa account?
I would first try to see if you can replicate the issue? Maybe there is a JS error that is preventing tracking from happening properly?