I used to play a game called Combat Arms. It used to (still does) come out with monthly content updates. After each update, anti-malware/virus/etc program would flip out. But only after I started the game. It would go something like this:
"An update, Oh boy!" Downloads, installs...
"Let's Play this new content!!!" Double clicks icon, game loads.
"Pick a server, any server." Picks server, room, and game.
"It's ASS KICKING TIME" (I wasn't half bad at this game by the way) Clicks join game.
Connecting...Connecting...
All of a sudden the game would exit from full-screen mode and jump to my desktop. My game session would have been disconnected and a dialogue bog would pop-up saying "Combat_arms.exe has been modified since the last time it was run. This could be dangerous for your computer. This software has disabled its ability to connect to the INTERNET. Would you like to allow it to connect to the INTERNET?" Of course I would click yes and re-join the game.
Of course the real kicker came one day after I went through this process. The game comes with a piece of anti-cheat software that is built in to prevent people from hacking the game and cheating. Well this program popped up and told me that I had been reported for using a utility to hack! Boy that pissed me off.
I haven't played the game in a while because of the whole thing stated above and because its in-game content system just sucks. I would work my pants off just to get a fancy new sniper-rifle, only to loose it in 24 hours.
That's about it for times I've been reported/banned. I am pretty young (as an internet user) so I haven't really encountered any situations where I would encounter problems with mods.