There are a variety of fungal or bacterial leaf spots common to southern magnolias - pseudomonas, phyllosticta, cercospora. Some are weather related and would not surprise me to find on evergreen mags at the limit of their hardiness range and after the strange spring weather much of the country has experienced.

Typically the recommendation is to remove or prune out affected foliage and stems and keep the area clean. If the problem persists, you can try a copper-based fungicide.

by recently planted.. do you mean recently purchased???

if so.. you might want to talk to the seller.. and ask them why they are selling diseased stock ...

kenb

I don't think they were diseased when I purchased them. I think I would have noticed black spots on the leaves. I've had them for maybe a month now.

Is there a downside to me using the copper based fungicide right now?

My Southern Mag got some yucky spots over this winter also. It's first winter it looked great all the way to spring, though.