Connection timeouts when using NextDNS

I have been using NextDNS for close to a year now on all my devices. Last night I left my laptop in sleep mode and when I woke up to day to work, I could not connect to Clockify. Brave search too was not connecting with both timing out. On the bottom right, it was just showing 'connecting to clockify...'  I updated my Arch install and rebooted it. Same thing. I use network manager to set my dns settings and these are the contents of /etc/resolve.conf:

# Generated by NetworkManager
nameserver 10.0.0.10
nameserver 45.90.28.16
nameserver 45.90.30.16

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10.0.0.10 is a LAN server that resolves a domain used in my homelab. It uses Bind9 with NextDNS as upstream. Removing 10.0.0.10 only makes my domain unreachable and does not solve the problem. I tried having my domain resolve in NextDNS, but it only works on mobile and not on desktop for some reason. 

I have tested in Librewolf, Floorp, Firefox and Brave. Any configuration that points to nextdns does not work. So far it is only those two domains that seem to have an issue. I have tried DoH and that doesn't work either. Switching to other DNS providers solves my problem instantly. 

EDIT: I am seeing even more domains that are failing to connect as I keep using the system. It is becoming unusable.