When the guy is proning on bomb to defuse it (he has his head nearly in the crate) its impossible to kill him with a gun, only knife or nade can get him.

This remind me when the guy is 999 in spawn and can be hardly killed with gun... but here you can put a full clip on the guy defusing - he is never hurted, its a pity when you cover the bomb with a sniper a mile away I have never experienced this on match but at least 5 or 6 times on pub. Let me know if im wrong somewhere or if i missed something

Well, if the head is in the crate then shoot the body. All we know is that it is a glitch where limbs sometimes go through objects - especially in OBJ mode and with regards to the bomb and crate.

eheheh, no. I will try to get a video for that, and there is nothing to do with the head in the crate, you can shoot the WHOLE body with one ak clip + glock nothing happen, the bullets just go throuh him, there is no contact or anything...

Can't objects in maps be fitted with a null invisible mesh to prevent glitching into it?
I know in Infiltration they had a weapon collision effect , perhaps this can be done in a modified way in TC:E?

maybe, but this glitch is present in nearly every single Quake3 based game. TCE isnt the only one.