During Chapter 3, "Issei" talks about some of the most common ways a hero usually dies from and mentions that women cause a good number of heroes' deaths. Motoyasu berates him for being a paranoid nutjob. Come Chapter 27, five days before the 2nd Melromarc Wave and he's level 49 (he was level 43 around this time in canon), and mentions that he goes the extra mile to hunt monsters solo at night. Why was he doing this? That's because Motoyasu, albeit subconsciously, actually listened to "Issei's" Properly Paranoid back in Chapter 3 and spent less time fooling around and didn't have sex with Myne.
The author later mentions that he made a slight mistake at interpreting Motoyasu's character by thinking he never had sex with Myne in canon, although it doesn't really matter in the long run. That and you can just Hand Wave the whole thing by using the above explanation, as one reviewer notes.
In Chapter 30, we get to see Rin and Luvia from a different timeline than the one Shirou came from. Luvia drops the issue when she realizes it isn't her Shirou, but Rin continues to voice her concern to Zelretch. It's also implied that this is a post-UBW timeline as that is the only route that explicitly shows Shirou attending the Clock Tower. Once you connect these two information, suddenly it makes perfect sense for Rin's concern for Sword!Shirou as this isn't the first time she encountered an alternate version of Shirou.
When Naofumi talks about the [Companion Series] in the Church of the Three Heroes, Itsuki tries to dismiss it by saying there wasn't a weapon series like that in the game while Motoyasu surprisingly asked how to unlock it even if he doesn't like the guy. At first, it can be explained as Motoyasu putting into practice what he learned from Shirou, but as Chapter 43 reveals, that's because he unlocked a Weapon function on his own sometime after his talk with Shirou, which is why he didn't immediately dismiss the possibility unlike how his canon counterpart reacted during a similar situation at the start of the Cal Mira arc.
The whole Demon of the Sword stunt that Shirou pulled might be seen as suicidal and Out of Character at first as he is from a Heaven's Feel timeline, which would mean that unlike his Fate and UBW counterparts, he's not going to get himself killed since that would make his loved ones sad....until you realize his goal is to solve the world's crisis as soon as possible so he can get back home faster before said loved ones realize he's gone.
Back in chapter 13, upon first meeting Azu, Jian jokes that Shirou unlocked the "Harem Series" followed by adding Azu to the party, to Shirou's chagrin while wondering how she even knew about the word "harem". Around 30 chapters later we get Tyr's mini-chapter that reveals he pressured the Legendary Holy Sword to add his daughter in his party. It's likely that he slipped a comment or two about Shirou having a harem while doing that.
