Ya know, I've been using "glitiches" for years in other games and havent found any real adverse effects to my players. Now granted, the glitch/whatever usually is the result of a players bad choices. For example, I had an old Star Wars D6 game with a house rule concerning the "wild die". Long story short, player rolls a 1 on the WD, they tell me. I roll a d6. On a 2-5, its usually something that will complicate things like a blaster powerpack going bad, etc. On a 1, its considered a catastrophic failure. On a 6, the player succeedes despite themselves.
One example, a Jawa player is running from CorSec through an alley, decides to dive through a conveniently open window. He failed his roll and roled a 1-1 on his wild die: the result: his aim was off and smacked the side of the building. And he only had a 1d+2 for strength to resist damage...and rolled a two. Night night.
Second example, something more SR-ish. PC is in a club, chatting up a hottie he homes to schmooze for some info (and maybe something more). He's too busy trying his spheel and the club is to noisy that he misses that the hottie in question has been trying to tell him she has a boyfriend....a very BIG boyfriend who is now standing behind him about to put his fist into his face.
Third example: Sammie Ben Strong is trying to jump on a moving remote-controlled tractor trailor as part of an infiltration. Now, he misses, and misses BAD. He falls to the ground, absorbes the damage, but glitches. OK, how to handle this. Hmmmm how about the SMGs he was carrying suddenly go off because the impact had that one in a million thing happen where the smartlink egaged the remote firing command and now an entire mag had been emptied. Think of that scene from Im Gonna Git You Suka.
Fourth example: group of runners makes some INSANE stealth checks to remain undetected in a warehouse, but realize their ride is now compromised and have to secure alternate transportation. They hotwire a van, but glitch. The result: the vehicle reverse alarm, you know that BEEP BEEP BEEP, goes off and every sec-guard knows where they are. Oops.
Thing is, I use glitches not to punish the players, but most often as comic relief unless the glitch in question is something that would REEEEEEALY F-up the senerio. Its like in every TV show or movie where the hero has a "oops" moment. I can see how it could be abused, but if you have a good GM, then they can be quite entertaining for everyone.