Sometimes the autofill prompt appears at the top of my gboard keyboard when I’m logging into a website/app but often it doesn’t. Occasionally this is rectified by hard closing the app/browser and reopening of, but not always.
I often experience the same problem, exactly as you’ve described. I’ve found that I can sometimes force it to appear in Firefox on mobile by pressing the little shield icon to the left of the address bar, then pressing elsewhere to dismiss it.