In debug mode, Flask’s reloader will load the flask app twice (How to stop Flask from initialising twice in Debug Mode?). I’m not sure why this is, but it causes apscheduler’s jobs to be scheduled twice. A quick print "loaded scheduler" right before sched.start() confirms this.
There are a couple ways around this, as mentioned in the linked answer. The one I found that worked best is just to disable the reloader like so:
app.run(use_reloader=False)
It means I have to reload my app manually as I develop it, but it’s a small price to pay to get apscheduler working.