1. It's possible people are confusing Day 2 with a second day at the Academy. (Day 3 (Perhaps not- I haven't had such an issue.))
2. The options do not appear. He makes the suggestion, and that's the end of it.
3. The three lines prior are "Or you could...", "Well that's very forward.", and "That just seems to be his personality..." And then the following line is "My new dorm wasn't..."
~Second of the three aforementioned messages; I didn't get a screenshot.~
~As you can see, it just sort of skips like this is the line that naturally follows.~
4. Another thing, I know that in past versions, Qrom was one of the contacts. Has this been removed for the current version?
5. Don't worry about it. Just as any new game, there will be errors, whether they're something minor like a failure to load a background, or something major like deleted saves. I took this into account, just as most other players did, when they downloaded the game.
6. I do apologize for not submitting the error through the correct forms (Didn't see the text in the game description until just now.)
7. Suggestion. Perhaps add the option to decline Silas' offer to hitch a ride to the academy, in addition to the charisma check, so that players don't have to only follow the current guidelines, which you kind of have to accidentally stumble on. Take me for example, I wouldn't have known about it unless I read through the comments on this page. And, considering this is a gay, furry VN, the majority of people will choose either "Love", "A Lover", or "A friend" for their first route, and some won't play a second until the game is completed, if ever. As I said, just a suggestion. If it stays as it currently is, it will be like a secret route that's not super secret.