With Autopilot, you have 3 options.
Option 1:
Create device group and assign all the applications. So that when user log in to the device they dont have to wait for user level apps to install.
Option 2:
Assign apps to device group that are common to all devices.
Assign apps to user group that are specific to user profiles/titles.
Option 3:
If you know if a device is going to a device user (with a specific title)
Assign all apps to device.
Use auto-pilot preprovisioning and install all apps before device is shipped to user.
With this when user logs in the apps are already installed.
Note: This approach requires that you are changing your process completely. Also it requires you to integrate with Intune & most like Hybrid domain join.
Easiest option i see in your case,
- The app and software that are missing on the PCs,is it consistent everytime.
- If so, make a list of those apps.
- Check your SCCM image and see if the Task Sequence still have them in the list.
- Try to install the apps manually using sccm and see if they install.
From here i would get a fair idea on next steps.