This article on linking to specific spots in a longer text may help you out. It’s more a technique for encountering “X relates to Y” type links though, where you want to pick out a few specific spots that are related and make them easy to jump to in the future. It’s not so good for “take me to all of the many potential Y’s that may exist in this group of 50 documents”. It kind of sounds like that’s what you’re going for from the description. If so, I’d keep using the standard Find tool to jump from one hit to the next, and consider perhaps making use of some of the techniques described in that post to make the really important “undermind” instances easier to get back to in the future.
You probably had your keyboard focus in a Corkboard or Outliner view, where Ctrl+F brings down the filter bar for those views, instead of the standard text find tool.