Fires do (and are supposed to) take oxygen out of rooms if you still care, it's only sensible.
And most of this stuff doesn't sound like bugs. Beacons/sector maps shouldn't change, so that could be a bug, and if you are often reloading saves, it's a somewhat known one, but it's hard to say why it happens. There are more issues with the save system, really.
Crew killed on the flagship.. depends how they died. If you really kill them and finish off the ship, they should be dead. If they were only in a wing that fell off, depends on the difficulty. If they didn't finish their death animation.. I'm actually not sure. If you jumped away yourself, I think it depends on which stage you're on.
Damage to enemy systems could have also happened from a fire. Screenshots would be useful if you saw it happen again, can't think of much else you could miss, maybe a bomb damaging your system.
Enemy ships are impervious to your damage after you accept surrender, it's normal. However, the only time 'never surrender' comes up in the texts is the slaver event when you can give up your crew, and the text happens before any fighting can start. You should be accurate about the events if there's something you think is wrong.
Having a Continue... twice in a row is fine and not uncommon, again not sure why you think it's a 'bug'. The event simply has more to tell/give you without too much 'player interaction'.
Anti-bio beam damage crew on the tile they hit (there are 2-4 tiles in a room), shouldn't go through shields, but you're too vague, I'm not sure if you meant zoltan shields, normal shields, or what. They are capable of breaking zoltan shields quickly if you shoot them as a shield drone brings up the shield. It doesn't do any damage to rooms at all, however. That's what I mean, you have to be exact.
And agreed with stylesrj about the wikis, there are two, ftlwiki is very old, ftl.wikia is more useful, but still often not even close to reliable, let alone comprehensive. Tables and stats are mostly good there, but for this kind of information, you're likely much better off referencing a guide like this:http://steamcommunity.com/sharedfiles/filedetails/?id=266502670
It has a very large amount of information in it, though you may have a harder time searching.