I made a mistake. I used Tor proxy in Firefox settings to access the web through Tor, but I forgot to check the Remote DNS. Tor logs warned me that some of my applications may use their own DNS. The DNS might be from my location, in my case Firefox browsing going through Tor. Do the DNS servers get aware of my clearnet IP address or just the exit node's IP?
Tor is saying that a program did not use DNS through Tor and instead used DNS through your clearnet IP address. While the DNS server, and those that saw your connection to the DNS server, do not know what you did on the website you connected to, provided there was an encrypted connection to the site. They may be able to figure out what you did on the visited server using a timing attack or something similar.
If you perform a DNS request for google.com through your clearnet IP Address, and now your DNS server now knows you visited google. They don't know what you did directly however.
When you visit a site and it performs a DNS request through your clearnet, your DNS server does know that you were trying to contact the server, website, in some way. (e.g. ping or viewing a webpage)