For reference, logs for the OP indicated it’s most likely caused by the ISP intercepting DNS packets. I haven’t noticed any message from protree yet.
There is one elusive unsolved issue. It only causes occasional problems for some domains AFAIK, so if your DNS doesn’t work at all (not clear from what you write), it’s probably something else. Forwarding should work around the linked issue, but that setup is sensitive to “quality” of the forwarded-to servers, and with ISPs it relatively often leads to problems on some names. (They tend to use BIND versions that are several years old and thus buggy around some edge cases.)
You may also like Using dns over tls or https, but there you give your data to yet another party, so it depends… I don’t think any of the options is always superior.