Gargoyle Removal Service
If you convince the gargoyle to ally himself with Isaac, go and tell Isaac (which completes the quest) but then go back and destroy the gargoyle, the quest re-activates and tells you to inform Isaac that you killed it for him. The dialogue options to do this are gone, so you end up with this quest entry stuck in your logs until the end of the game. You do get some nice extra XP this way though
Character Info
If you go to your character sheet and click on "Info" at the top (there's probably a quicker way to get there, but whatever) the text that describes you clan doesn't word-wrap, meaning you only see the first line, then it continues outside of the box meaning you can't see it.
Werewolf Fangs?
I don't know if this is a bug or what, but why does the werewolf have vampire fangs? This may be normal of course, so sorry if I'm just saying silly things
DMP worker dialogue
The scared DMP employee is killed while still telling you to rescue him, because the creature attacks after you finish talking, not after he does. (adding a "..." final dialogue choice might fix that, but I don't know the first thing about modding so ignore the suggestion if it's absolute crap)
Um... anything else...
Well you already know about the card machine 'use' boxes thing, so I think that's everything. Thanks for reading
edit: The I Spy Barabus quest leaves a log entry for me at the point of it telling me to go to the Red Dragon to meet Wong Ho, even though I've done that quite a while ago. (in fact I noticed this log entry after coming back from the Giovanni mission)
edit again (and I promise this is the last one): In the Tutorial, at the very end, Jack turns around so that his back is to you, but then turns around again to be facing you when he finishes talking. Like the other bugs, this isn't important, but hey, why not mention it anyway