Then i remembered that the source abomination did some weird water attack in a random direction and i thought the heck was he aiming for and tried to reproduce it.
Ahh, so this is a bug - glad you've reported it as well.
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Bug: Mechanics
Priority - Medium
The 'waterspout' attack [crabs, large source spider, source abomination in black cove] is currently broken. The targeting plane is miles in the air, and it never does any damage. Comes with added graphical glitches!
This is probably related to issues with cone spells / planes as well.
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Your crate problem looks like an issue that has plagued alpha / beta, which is quick-saves not restoring world objects correctly. I've not come across it this play through, thought it'd been squished. In my play through, the crate was alive.
