I found a solution to the problem in the title that I’m sharing for others like me.
This was an extremely annoying bug to work through. All of a sudden, when I created a relationship between two custom queries, it said “no matches found”.

Solution: When I created a relationship field in a field group, ACF created a second field with “(no label)” and only the “field name” filled out correctly.

Just fill in your desired info into that 2nd field group, change ‘text’ to ‘relationship’, and delete the 1st one you created.
Hope this helps!
Heads up! The reason I got this bug in the first place was because I was creating a Chrome extension and had “developer mode” on. After I turned it off, everything went back to normal in all my plugins.
I guess developer mode autobreaks JavaScript as a security measure?