We apologize for the overdue response. Thank you for the multiple photographs. At first glance it appears that a few branches are failing but upon closer look, the newer growth at the top of the tree looks like it is starting to discolor and brown.

The digging/dividing perennials under and around the tree might damage some roots on an older tree, but this tree looks fairly newly planted. You would also likely have known if you cutting into any larger roots while digging. So that is likely not a problem. 

When was this tree planted? Was it purchased in a plastic container or balled-and-burlapped in a wire basket? 

Most magnolia do not like wet soils and we have had a lot of rain this season. The way the leaves are starting to discolor on the new growth throughout the canopy, it does looks like it could be a situation with the roots, including possible too wet of soils. However, I see some plants in the photo under the tree that would don't like water-logged soils either and they appear healthy. Have you noticed wet soils while digging recently? 

Also, sometimes when a tree is planted in more slowly draining soils (if different than it was growing in a nursery), the water can sit in the root ball area and not move out quickly enough and essentially drown the plant. Could you dig a bit around the top of the root ball and see if the soils are wet or dry?

It would be really helpful to see what is going on with the trunk. Would you be able to take and send a few more photos of the trunk and where it meets the soil? 

Is the root-flare (where the trunk and the larger roots meet and start to flare out) buried? This is unfortunately a very common problem with nursery grown trees and can be problematic if not uncovered when planting.

There could also potentially be a borer issue on some stems, but this seems less likely. Can you take a look and see if you see any small insect exit holes on the stems that have browned?

Thanks for sending more photos. The way the whole tree failed quickly, there is clearly something impacting the tree's ability to move nutrients and water throughout the tree. 

It does appear that the root flare is buried and that could be a contributing factor. You could also have a girdling root below ground that is essentially choking the tree out. The hybrid Elizabeth usual grows quite tall with vigor. There are often multiple factors that eventually lead to a tree's failure. It would seem as though this tree may have been stressed for some time. Some combination of a buried root flare, girdling root, and wet soils are all stresses that would explain why it has grown so slowly over the last 15 years.

When you dig up the tree to remove it, take look at the roots right around the trunk below the soil to see if you see a girdling root. Take a look at how deep the wet soils seem to go too.

The suckers at the bottom of the trunk are likely not the same magnolia as the top, they are probably root-stock that the top of the plant was grafted onto. They won't grow up and become a new Magnolia 'Elizabeth.'

Wilts can display symptoms like this. One that can sometimes attack Magnolias is Verticillium Wilt. You would need to confirm diagnosis of this by a diagnostic lab. Note that for verticillium wilt you will need to send in a specific type of branch sample, as instructed in the lab link below. 

Here is a link to MSU's diagnostic lab's website:

Plant & Pest Diagnostics (msu.edu)

Here are links from MSU with more detailed information on this issue:

Verticillium wilt refresher - MSU Extension