Hi,
So unfortunately, not a great thing to deal with.
1. Licenses are assigned as apps are Shared with them, so you have to keep track of what security groups (yes I am saying DO NOT have people just randomly add people as that makes this `1000000 worse), that apps are Shared Too. this way you can more readily keep track of... sort of who.
You could do this by going through each Group that is used to share with Apps, and do a count of people. You could also verify if the group is actually being used by going through each App and seeing who its shared with...
When people leave your organization etc, you need to make sure they are removed from the Groups that are used to share apps, and OR if they are individually added.
So you will see a Count across your environments of usage, but its up to you to (I know it stinks) to create a process to track who you are sharing apps, where environments are setup for Per App Settings
That is the best answer right now. Microsoft IS working on something to cover consumption reporting, but WHO knows when it will be there.
Until then to the best of my knowledge what I said above is accurate.
And to NOTE, I do NOT normally respond to licensing things because of how they are... but the above is the way in which I handle it and after checking again, appears to be the only way to really do it.