In "Terraformer", the Twelfth Doctor tells people to hide behind a couch if they're scared.
In "The Weeping Angels of Mons", the Tenth Doctor alternates which of his eyes is open to constantly be watching the Angel, something the snarkier aspects of the fanbase were ruthless to point out in the Angels' first story.
At one point, the Twelfth Doctor is cut off while telling Clara "Don't forget to subscribe-"
Issue #5 of Four Doctors was delayed by a few weeks, being released on September 23rd instead of September 9th. Rather ruined the promise of a five-week event.
Supremacy of the Cybermen is hit with this badly. It was supposed to last 1.5 months (July 6th to arrive August 31st 2016). Issue #2 was released on August 17th and further delays meant that the whole thing lasted five months.
"A Little Help from My Friends" was to run from January to April of 2020 but its final issue ended up being delayed until late May of that year due to the COVID-19 lockdown.
The rebranded series Doctor Who Comic (2020) was supposed to launch in June but was pushed back to November.
What Could Have Been: Originally, before her dramatic departure in Series 9, Clara was going to be the companion throughout all of The Twelfth Doctor: Year Two.
Word of God: The writers try and avoid having Rose meet other companions because they know they'd have to have a Clingy Jealous Girl moment which they feel detracts from the story.
Writing Around Trademarks: As a result of the complicated relationship between the Nation Estate and the BBC, the Daleks can't be used freely in the comics. The Volatix Cabal gets around that by simply not putting the squids in casings and having them not act 100% like ordinary Daleks.