NTP, BGP, MTU and a lot of other acronyms should be also in the list of not trivial to trace root cause for things that goes from big outages to mysterious malfunctions, specially if there are many parties or servers involved. And the security protocols that are above those and more (DNSSEC, SSL, etc).
Shit can and must be troubleshooted with domain-specific tools.
DNS: I do have an ongoing problem specific to Unbound where it refuses to serve some entries in a transparent zone of DHCP-registered addresses that have written to config files properly but it insists on refusing to resolve certain hosts nondeterministically. But that's the only problem I have had in a long while because mostly infrastructure works out of necessity and scale.
