Here's what I caught, in order:
"This could take a while Fish" needs a comma after "while"
"do you think she'll really go for this 'distraction'." needs a question mark, not a period/full stop.
"she's a computer, multi-tasking is" That comma should be a semicolon.
"entity he was about to face. Changed" There should be a comma instead of a period/full stop, and the subsequent capitalization fix. Fragments, you know. If you want to keep it a sentence, add "She was" to the beginning, and a "they were" after that sentence's "but" couldn't hurt. Additionally, "originally" may be a better word in that sentence than "effectively", considering that Evie is no longer the same as GLaDOS.
"GLaDOS'" should be "GLaDOS's", since there is only one GLaDOS in the area at the time.
"(well, it does sort-of" should have a comma after "does".
"reality-warping entites" should be "reality-warping entities"
"She's not all bad really." could use a comma after "bad".
"Oh, are you finished." should be "Oh, you are finished." or "Oh, are you finished?" I'm not sure which you were going for.
"your sort of thing though really" needs another comma after "though".
"the AI spoke with almost visceral disgust" should either capitalize the T in "The" or change "spoke" to "said".
"worm like construct" should have a hyphen between the first two words.
"superheated plasma he shot" needs a comma after "plasma"
"He emerged in a heap in one of the control rooms" is confusingly phrased. Maybe "He emerged from a heap in one of the control rooms", but you do not emerge while in a heap. It's like "grinning" a line of dialogue. It is hard to do.
"it on. "Missed me, GLaDOS. Now, listen" You could do worse than starting a new paragraph when the Fisherman begins talking.
"status-quo" should not be hyphenated.
Another "GLaDOS'" should be "GLaDOS's".
"Me, oh I'm just a" should be "Me? Oh, I'm just a".
"walkie talkie" was hyphenated a few lines before. I've seen it both ways, but pick one and stick with it.
"exception occured" should be "exception occurred"
"main facility intercom" I don't know the context, but "facility" should probably still be "facility's".
"Us two; two other humanoids, the DoSAT techs I imagine, and twenty-three" This is a tricky one. I could say remove the semicolon and make it a comma, but "the DoSAT techs I imagine" could be considered a separated phrase. If it is, the rule would be to make the comma before "and" another semi-colon, but that doesn't look right to me. Deal with this how you feel is best. Maybe just ignore it even; it's not that huge a problem.
"heard that fishface" should have a comma after "that".
"near darkness they had" needs another comma after "darkness".
"Well, Xylander had shut himself inside and refused to come out and" The "Well," is unnecessary and should be removed, and there should be a comma after "out".
"remember you Xylander" should have a comma after "you".
"Test Chamber 05, that should" There should be either a semicolon or a period/full stop after that comma. "He'll have a Remote Activator, you'll just need" has the same issue.
"Makes sense seeing as he is one." should have a comma after "sense".
"moment the techies" should have a comma after "moment".
"Now, where are these ypurs." should end in a question mark.
"a group of three ypurs and pressed" should have a comma after "ypurs".
"Don't tell me it's broken," Misa sighed." That comma should be a period/full stop, and it is very hard to sigh a line of dialogue. It's not as bad as grinning it, so you can keep that if you can't find a substitute, but it bugs me.
"white tiled" should be hyphenated.
"to get the things over here somehow," Xylander said" should have a period/full stop not a comma.
"next ten minutes they prodded" should have a comma after "minutes".
"Chamber 09, head there next," Evie replied. "Bad news is that you'll have to walk it, there aren't any" has two commas, one after "09" and one after "walk it" that should be either periods/full stops or semicolons.
"day just gets better and better," the Fisherman sighed." has a comma after "better and better" that should be a period/full stop, and there's that sighing-a-line-of-dialogue problem again.
It's a lot, but I don't like missing typos in the reports, and I've been getting annyed at my previous two SpaG reprts being lackluster. Also, I don't know if you use the term "period" or "full stop" to refer to the end-of-sentence dots, so I used both, as you could see.