Regarding Ancient pheonix bug, I may be referring to a different bug but when you get the option to resurrect your pheonix and you choose not to, the pheonix stands up at least it's image, it is still dead and units can walk on the tile where it died. It is a graphical bug, it doesn't affect the game in any other way.
I've seen highterant lay an egg in a inaccessible tile (the void in gremlin battle).
Another bug I don't think has been reported is when evil beholders mind control one of your units it stays mind controlled for 2 turns instead of just 1. In my experience it should allowed to dictate one action of the target, not control it for 2 turns.
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