You can force sync comments by going to the original instance and getting the /comment/#### link, and searching it in your own instance. It could be possible to automate this via the resolveObject API call, but a lot of people doing it en masse wouldn't be good for the big indtances.
It boils down to either your instance not using with workers to handle activityhub updates, or the big places being overloaded and experiencing the same thing. If they don't get to successfully send you an update, or you fail to receive it in time, you miss out on that content.