Hi Lori,

Thanks for contacting the UNH Extension Infoline about your Magnolia tree.  I am not familiar with this disease but have lots of resources to research problems like this.  

Typically, I would encourage you to cut out a sample and send it to the UNH Extension Plant Disease Lab but unfortunately, it is temporarily closed. Some people are sending things like this to the lab in Maine; here is their link. I can't promise anything as their first responsibility is to Maine residents and commercial growers, but it's worth looking at their site and contacting them. Then you would know for sure what this is. https://extension.umaine.edu/ipm/plant-disease/ 

From the helpful photo's you sent, it looks possibly like Black Knot but no sources I find say this is typical in Magnolia's; it is common in stone fruit trees like peach, plum, etc.  I'm wondering if you might have some of those nearby and if so, do you see this growth in them as well?  If so, that might be a good clue.  

Common issues with Magnolia are scale, funguses, viruses and bacteria- all can show up in leaves, on branches or in overall health of the tree.  Since your tree is not in leaf, it's hard to know what else might be going on.  It might help to cut them out (cut about 3-5" below the growth) and make sure to burn the cut branches or dispose of them at your curbside, contained, so as not to spread to other areas/plants in your or your neighbors yards.  

In the meantime, I've also attached some resources about Magnolia and typical problems that I hope you might find helpful, below.  I'd compare their descriptions (both from last year if you remember or have photo's- these things often progress through different stages which can appear quite different- and what happens if you don't remove them or after you  do remove them) and images provided in these info sheets/articles, to see if you think it looks like Black Knot.  I cannot find another disease that looks like the sort of flaky black one's from you photos.  They are quite distinctive.  

https://hort.extension.wisc.edu/articles/black-knot-apiosporina-morbosa/

https://plants.ces.ncsu.edu/plants/magnolia/

https://extension.umn.edu/plant-diseases/black-knot

And this is a long shot...  Some photo's I found of the seed of  Magnolia grandifola, not commonly grown up north due to being a zone 6 plant,  look a bit like what you've shown.  Especially their placement which appears to be at the end of branches.  Again, only if by chance you have this type of Magnolia tree.  Photo's below are in different stages. 

I wish you the best of luck and apologize again about our plant diagnostics lab being closed.  

Catherine