Harsher in Hindsight: Caren's line "Stop? Or what, you'll violently rape me? That's a bit out of character for you, isn't it Shirou?" Later on, Shirou -actually Angra Mainyu possessing/disguised as him- violently rapes Caren.
Ho Yay: Issei and Shinji both have points where they are practically competing to see who is Shirou's best friend, at time actually fighting over him.
While Rin is romantically attracted to Shirou, when her date with him at the pool is interrupted by Rider, Rin admits she and Shirou both noticed the same part of Rider's body. Rin goes on to note how beautiful Rider is and how she feels inadequate in comparison.
While Caster avoids any of her Depraved Bisexual moments from the original visual novel, she still expresses a desire to see Saber try on various outfits, this time only being played for laughs.
Moe: Caster of all people manages to reach this status, sometimes reaching Tsundere status.
Both the backstory of Princess Medea, the Witch of Betrayal (aka. Caster) and the recounting of one possible route of the Holy Grail War (not one of the potential canon ones from the game) where Gilgamesh attacks the temple, mortally wounds Kuzuki, and leaves Caster to grieve over his dying form.
Technology Marches On: Subverted. Several characters mention receiving an "anaconda of a fax" from Tohsaka containing the lengthy script of the School Play the archery club intends to perform for the Cultural Festival. This may sound anachronistic for a story set in 2004, but it turns out that fax machines were still very much in use in Japan then and even ten years later for a variety of reasons.
They Wasted a Perfectly Good Plot: You might expect that now the Holy Grail War is over (and almost all the characters are inexplicably still alive) they'd take the time to explore Archer's backstory, particularly what he went through to turn him from the idealistic Emiya Shirou to the cynical Archer, as well as how he's dealing with being back in his own past, seeing people he knew from his youth again. You might expect this. But apart from a single scene where Those Three Girls mention that Archer seems strangely familiar for some reason, you'd be completely wrong and Shirou and Archer just continue with their usual offhandedly antagonistic relationship. This is because, at the time, the Archer Spoiler™ was considered one of the truly great sacred cows of the franchise and every single effort was taken to conceal it for people who hadn't seen The Reveal in the original game. Yes, even the fandisc sequel still tries to hide it. Fate/EXTRA took similar steps to conceal it. Nowadays, with Fate/Grand Order casually spoiling it, it looks especially silly.