Do rubber septa from infusion bottle need to be disinfected before preparing an infusion?

Yes.

Background:

Rubber septa from infusion bottles must be disinfected with an alcohol-based disinfectant before inserting the cannula unless they are already sterile. Pursuant to the Robert Koch Institute, alcohol-based skin disinfectants can likewise be used for this purpose.

References:
KRINKO (2011) Anforderungen an die Hygiene bei Punktionen und Injektionen.
Bundesgesundheitsbl, 54:1135-1144.