I experience this a lot. I suspect the main cause is the general crappiness of my computer. But if dangerous abilities that you must be able to react to in a timely manner could somehow get cached before a bossfight starts, or they could otherwise be prioritized, it might help.
I've got Intel Core 2 Duo E4400 processor and I understand it's on the verge of not being able to run this game properly. My GPU is GTX 560 Ti, so it's definitely NOT only a problem with ATI cards. The latest nvidia driver update helped quite a bit with my framerate issues, but the "invisible abilities that kill me" -problem doesn't care about what drivers I am running.
In many (or most) fights I can only start seeing some boss abilities after a short delay like 10 seconds, which can often stretch, to about 30s at the most. Sometimes there is no delay at all. It seems to be tied to the time a boss first uses a specific ability, and if we wipe and have to retry the fight I usually have to wait to see abilities all over again. And another thing, I think I have less problems with first pulls on a boss after a tactics briefing than others, but I'm not sure of this. It's just something I've thought of recently and I haven't really tested..
Stuff I have problem seeing:
Soa - the green aoes he does at the start of the fight
Foreman Crusher - red circles on the ground where the rock he throws will fall (this was vey annoying when we were learning the fight)
Karagga - Mouse droids, gravity vortex, and I guess the fire too, but I'm ranged so I'm not standing close to where it spawns anyway.
Zorn and Toth - The yellow circle signifying the target for the big rock throw which can end Toth's enrage.
Firebrand and Stormcaller - Yellow targeting circle from firebrand and the storm rods from stormcaller
The last boss in Lost Island: in first phase, the circles on the ground where poison will be thrown, and the poison itself.
There are many others, these are just some that came to mind. Probably because they're been rather annoying to deal with.
And err, workaround? I often have to rely on my guildmates yelling at me on Mumble to avoid these abilities early on, or, if it's icky stuff on the ground that does a dot the rolling combat text to show the damage you take can help some.