Android Market not showing full list of app updates
I realize this is an old question, but still today I face the same issue. The reason behind this (AFAIK) is that apps, when updated, can be "batch updated" if no changes were made to the app privacy policy or the app permissions for the device (other scenarios may apply).

e.g.,

Just this week I did a "batch update", but had to manually update two apps, one needed my consent for additional privileges, and the other one had changed something that I didn't bothered to read.

Message from the first app that was outside of the update batch:


  This app's permissions have changed to have access to the following: ... 


Due to this changes, this app was excluded from the batch update.