I am having the same issue with rate limiting. I have increased the limit to 2000, but got the same warning 24h later. I am not very experienced in this stuff, but perhaps you could tell me where to find out what is quering my router? I only have 1 pi-hole on a Rpi Zero w that is set as my DNS on the router and everything connects through that.
I have made a log with the command mentioned above:
Thank you for your help