With Autopilot, you have 3 options.
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.
Assign apps to device group that are common to all devices.
Assign apps to user group that are specific to user profiles/titles.
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.