I have noticed that occassionally the filters seem to run on a delay...I have filters to bypass the inbox and apply a label. I will see the email in the inbox for up to an hour before the filter runs and then later I see the label applied and the email is no longer in the inbox.
I've noticed the same on Spam filtering as well. It used to be instant but now more and more I see things show up for a few minutes before disappearing. I also just recently set up a new gmail account that required some filtering to a sizeable inbox and it was very painful because of the delays.
Considering the effort that goes into Google products (not to mention that gmail is a core product), it seems strange that in 2019 a feature like this is noticeably delayed.