This problem has now been fixed.
If it re-appears, here is workaround that I developed dealing with similar problems with the real-time API over the past couple years.
Set your system up to use both the real-time API as well as the search API as a fallback. Ingest data coming through the real-time calls, but also periodically poll the search endpoint (either media/search or tag/search, depending on your application) for data you might have missed, ignoring IDs your system has already seen.
Your system will be much more resilient to issues with the Instagram API and also allow restarting your system periodically without missing data (since you can catch back up to real-time).
I keep track of "seen" Instagram IDs in a Redis set.