I downloaded and installed the mandatory update for PS3 a week ago.
The game has gone wierd since then.

Enemies glow green sometimes.
Quests don't trigger properly, or are lagging in response.
A NCR MP male appeared and tried to kill me when I tried to wait 2 days for the response to ED-Es last data piece. He kept appearing whenever I tried to wait 1 day. He appearred in the middle of Helios 1 and Camp Forlorn Hope, for frags sake! He turned the forlorn hope NCR against me when I killed him! I am liked by the NCR!
I went to my room in Novac in the end and triggered him there, were killing him did not change my status.
He has not reappeared since, thank goodness.

Boone disapeared when I told him to go to the Lucky 38. He was in nowhere he was supposed to be, not in the 38 or in Novac.
He was away for a bit then he appeared in front of the door from the courtyard to inside at Gommorah. He has never disapeared before.

ED-E got stuck at some points. I had to send him away to get him to move!
Some parts of quests did'nt appear.

And the high level CL assasin squads! They spawn EVERYWHERE! They spawn in random rocky areas, they spawn outside buildings, they spawn were you most definately don't want them! I could'nt even drag Moralaz' corpse to safety in peace!
There used to be small ammounts of low ranking assasination squads but now theres these ridiculously and unfairly overpowered assasin squads everywhere!
I am guessing that the same thing happens with siding with CL. And other factions you annoy.

Boone tried to kill Oscar Valesco when he saw him Red Rock Canyon. He killed him in the cave but that was reasonable. I sent him to the 38 after I reloaded after trying to talk to Oscar turned into a fight twice. Then he disapeared. I think they are either meant to fight each other or a bug caused it. Boone said exactly the same thing as when he met him in the cave. So I think it was abug.
I have taken Boone into red rock canyon before, he never attacked anyone before or was attacked.

Rex sticks in doors more.

There were bugs and glitches before but they have got worse!
This update has caused bad things.

I think it improved it but it caused some bad things too.

Why the hell have they put so many unfairly high level assasin squads in the game! It does'nt need them!

Do you have Rex with you? His perk makes loot and loot carriers green when you press a certain key or button. Could it be that? Maybe it's glitched?

I'm not playing my PS3 version now because Boone was only half-fixed with this last Patch and I can use a mod on my PC version and he's completely fixed. I can't help with the other problems you're having but maybe someone else can? I like the Legionary Assassins but I always keep my companions with me; I've never fired one. Have you tried starting a new character to see what happens?

Part of that quest is Oscar becomes hostile if Boone is with you OR your wearing a 1st recon berret.

The only thing out of the ordinary I noticed was that Colonel Hsu does not remember me, as in, he begins dialogue by saying that he hasn't had the pleasure of meeting me. That, and apparently the patch that removes Motor Runners Helmet is not retroactive. Though that isn't really a bug.

This was a new character. I can say for a fact these things were all post patch because I put it in to start this character and it downloaded and installed the patch for over 6 hours. After a long time time I finally got to make her.
The damn CL assasin squads are appearing out of nowhere! I hate them! They make it so I can't play the game on normal when I fight them sometimes. I do have companions with me all the time. They are just completely unnessesery and ridiculously hard!
I did not know about Rex making loot carriers glow green. It could be that or it could be a bug.

Another thing. I get stuck on things more. In first person I get stuck on companions, furniture, anything! It won't change to third person and rotates to a limited degree and won't do anything else. I have to reload when it happens.

Companions are getting stuck more. I have to send them to the base or home or try to kick them out of the way or jump over them.

A good thing is I managed to do some companion quests I could'nt do before. I think the patch fixed them.