That can be avoided if you do the puzzle properly, expending the correct units. I am not sure if enc-none works (it doesnt in the japanese version, only reduces the encounter rate)
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matching up those colour dinosaurs in space.
that bloomin irritating prison
You're supposed to stand still when the light in the centre of the room is on.
The only part that really annoys me is the sewers in Deling City with Quistis and co. Mainly because they are stupid for being there in the first place.
And maybe the prison.
The thing I hate most though is worrying if I might have forgotten something that I won't be able to do again before going to disk 4. I like goin into towns :C.
oops yes, my response was to what you do to avoid fights with Ultima Weapon.
Yes you have to just walk at th right time to avoid battls with bahumut :)
same as OP, missile base is really where it lets me down, sometimes D-District prison can have that same effect. Even when you get back to Balamb it might be like that for me.
After that, though, and Squall wakes up, the White SeeD's show up to take Ellone, it all gets even better after that point for me.
Laguna's sequences at Lunatic Pandora and Winhill, and the D-District Prison. Which means I pretty much hate the start of disk 2.