Based on what I’ve been able to find, unfortunately there aren’t too many injured!Magnus fics – or at least there aren’t on A03. I’ll keep looking, but you could try these in the meantime: 

Demon Attack by deathdario

Chapters:

One-Shot

Genre:

Canon AU

Length:

Under 5K

Rating:

General Audience

Secondary Characters:

Catarina Loss, Izzy Lightwood, Jace Wayland, Maryse Lightwood, Robert Lightwood

Secondary Pairings:

None

Themes:

Angst, Hurt & Comfort,

Injured Magnus, Injury, Protective Alec

Summary:

Request: Magnus is attacked by a group of demons on his way to the institute and Alec struggles to cope when he thinks that he’s going to lose the man he loves. But then things get even worse when he overhears Robert and Maryse talking and realises that they arranged to have Magnus killed.

I’ll Be With You in the Dark (Give You Light When You’re Afraid) by siriuslymerlin

Chapters:

One-Shot 
Genre:

Canon AU

Length:

1K to 5K
Rating:

Teen & Up

Secondary Characters:

Camille Belcourt,

Catarina Loss, Clary Fray,

Izzy Lightwood, Raphael Santiago, Simon Lewis
Secondary Pairings:

Raphael Santiago / Simon Lewis

Themes: Domesticity, Established Relationship, Fluff, Hurt & Comfort, 

Immortality Issue,

Injured Magnus,

Injury, Protective Alec

Summary:

Magnus Bane has never been weak. He’s an all-powerful being, capable of great and mind-blowing feats of magic. He doesn’t need to be carried into his own apartment. And yet, here he is, gathered in Alexander’s arms, protesting weakly. Alec doesn’t bother listening to him, going so far as to hum tunelessly to drown out Magnus’s already too quiet words.

If anyone else has any recommendations, please feel free to comment. And thanks for the ask 🙂