Injections can leave marks. It depends to an extent on what the injection was for. If it was the myxo-RHD-vaccine, the most common side-effect is a local, non-painful swelling around the site of injection, max 2 cm across (not quite an inch). It’s harmless and should go away in a week or so.

Injections with Baytril can sometimes cause sterile abscesses. An sterile abscess is a pocket of pus that forms as an immune response to a foreign body. Since it’s sterile, it’s not bacterial.

Local shortlived skin reactions can probably always occur. How is your rabbit doing now?

Ok, thanks for the update! I’d guess the injection was ivermectin, a very effective and bunny-safe anti-parasitic.