These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Two defeating the Celestial Toymaker by cheating(?) at Crazy Eights.
The very concept of ten Doctors in the same adventure.
Fridge Horror: Several canon episodes set after this comic have the Doctor refer to himself as "the last of the Time Lords". Makes one wonder what happened to Drax and the Rani... and by extension, the two innocent companions travelling with them.
The Dalek conversions of the High Council, the Lady President, and the Tenth Doctor are a lot like Oswin's Dalek conversion in "Asylum of the Daleks". And the Doctor fighting off the Dalek programming is similar to Oswin doing the same thing.
Eight calls Nine "my successor" when saying goodbye, but Nine will NOT talk to Eight and leaves in a huff. Eight concludes that he will end up doing something horrible. Nine's anger makes MUCH more sense after "The Night of the Doctor" revealed that Eight willingly allowed his regeneration into the War Doctor — Eight's actual successor.
Speaking of "The Night of the Doctor," in that special, it is revealed that Daleks and Time Lords are regarded as more or less the same during the height of the Time War. In this fanfic, thanks to the Valeyard's experiments, they DID become the same.
Omega's plan to destroy the First Doctor, which would cause the Universe to plunge into chaos is similar to the Great Intelligence trying to destroy the Doctor across his time stream which would cause destruction across the Universe in "The Name of the Doctor". Which came out about 4 and a half years later.
Seven comments that the ramshackle alternate power supply for the TARDIS that Nine came up with post-Time War (and thus after Gallifrey and the Eye of Harmony were inaccessible) is "an explosion waiting to happen". This, way before the Eleventh Doctor is confronted to the problem in "The Pandorica Opens"/"The Big Bang".
Seven and Three commenting on a mid-life crisis about Nine is downright prophetic of "The Day of the Doctor", where the War Doctor ponders the exact same thing about Ten and Eleven.
Basically the same explanation for why the Doctors don't remember these multi-doctor events is given in "The Day of the Doctor".
While we're talking about "The Day of the Doctor," in that episode, the Curator (who looks like an aged Forth Doctor) tells the Eleventh Doctor that he'll one day revisit some of his favourite old faces. In this comic, the Valeyard, who is the Doctor's future dark side given form, regenerates into a younger version of the First Doctor.
Les Yay: Dr. Grace Holloway believes that Romana II is actually the regenerated Doctor, and leans in to kiss her. When she finds out the truth, she's... noticeably embarrassed. For her part, Romana mentions that the kiss was "nice" and later on mentions that Humans are the species that get hung up about this sort of thing, but it doesn't bother Time Lords. Les Yay, indeed.