How to cook squid to get rid of the 'urine' flavor? What causes that flavor?
According to this site and confirmed by several others I found on the internet, the Humboldt Squid produces ammonia chloride as a defense mechanism, or as a side effect of asphixiation, or maybe both.

I couldn't find terribly reliable advice on how to avoid the contamination, but two points were repeatedly suggested on various bulletin boards:


When you catch the humboldt squid, cut its head off, clean and ice it immediately (on the boat).
when cleaning it, be careful not to puncture the swim bladder.


The other suggestion repeatedly offered was to catch some other kind of squid.

Hope that helps.  For more 3rd-hand advice, search the internet for "squid ammonia flavor" and you'll see lots of bulletin boards and similar sources.