Here are some of the rules that came up in recent matches:

Model Placement

"Unless otherwise agreed upon, troops cannot deploy in a location without enough space to fit their entire base." - Pg 26 BRB

Here is one that annoyed me.  Played many a time and never been an issue until someone brought it up after the match (like 10 minutes after the match).  I asked the TO and he didn't see an issue until the player said that "the rules say".  He was right but TO said every meta is different and it should have been brought up earlier.  My opponent was not looking for a change in score but a better explanation to himself why he lost the match.  Heck...I lot the match before this because of the same rule.

I would say that you meed to discuss how flat edges should be discussed prior to picking deployment. If I was the TO and you did this AFTER deployment, I would agree the rule exists but say it's too late.

G: Mnemonica

This caused two issues Saturday at GenCon.  Neither changed the outcome of a match and neither would have resulted in a change ranking at the end.  I was right on both of them for once.

"If the host falls Unconscious, the original user’s WIP, G:Mnemonica and Lieutenant Special Skill may be transferred again to another ally who fulfills the same requirements (Cube...).This transfer makes the host go from Unconscious to Dead." - Pg 79 BRB

This is one that didn't effect me but my opponent had Scott from NY miss play it.  He realized it when he killed my Avatar and I removed it from the board.  It would have cost him 1 point for Test Run and nothing else.  He would have only beaten me for first by 5 points or so. It had no effect but it was brought up on the forums.

"You must identify the figure or Marker that acts as host, but not whether the Lieutenant Special Skill is transferred—that is Private Information—." - Pg 79 BRB

This happened to my.  Aaron (Plebeian) killed my Skiavoros and I was about to tell him who he was transferring too and he stopped me and said I didn't have to.  He was the TO and insisted on it.  The rule says that I have to tell him but not my LT.  I think he assumed because he knew it was my LT that he shouldn't know.  I think RAW means I tell him.

"The user may transfer his own WIP Attribute, along with the Ghost: Mnemonica Special Skill and the Lieutenant Special Skill (if applicable), to any other trooper in the same army that is on the battlefield in the form of a figure or Marker and has a Cube.

The new WIP replaces the host’s original value- Pg 79 BRB

This is one I forget about. It only screws me not anyone else but I usually run The Anathematic and Skiavoros in the same list.  This says that I can transfer both WIPs because they are both models with G: Mnemonica.  This is important because it can really boost your specialists.

Targeting Null

This something I thought wasn't in the game any more.  It's was very common in N2 where you would FO or data scan an unconscious player.  I swore it was in the book but I couldn't find it in a game and the TO said it was legal.  Came up the next game and my opponent (Jake) thought the same as I did but the TO corrected us.  If anyone knows the page to confirm or disprove this, let me know.