I've tested on both the Incursion and Chaos 3 versions, and only the C3 (possibly C5) Buried Bastille has mana drop into the water. I opened all four chests for the initial 2400 mana, and only the two overlooking the water had one fall out and become unattainable. There is no problem on Waves 2-5 as far as I know.
What I did:
My first tries involved standing on the wall behind the chests in the center of the map and opening them. I typically saw one gem fall out of reach. I thought maybe I was attracting them and causing them to fall. Therefore, I tried running up to the chest, opening it, and backing off without grabbing anything. After a few seconds I picked them up, dropped the excess, and got the rest. I had 2300 total most of the time.
I have a couple conjectures for why this happens:
- The most probable is the sheer number of gems dropping around the chest, all fighting for space.
- The walls aren't high/thick enough to prevent gems from spawning on/behind them. I say this because the Crystal Cavern and Prison Path chests don't have issues (the latter having some spawn on the window with the impaled skeleton).
This is just me, but I think the best option is to nudge the two central chests away from the death water. Other ideas include altering the hitbox of large green mana, changing how chests toss out mana, or messing with the map's collision programming to make the specific walls thicker, even if they won't look that way. Whatever the fix, please keep it in mind whenever a map with death pits and high starting mana comes around.
Workaround: open the prison or cavern chests, or stand right behind the central two and open them.
(Bonus: While failing maps to reload and replicate the bug, I noticed my Dryad's victory animation plays when a core is destroyed. Unsure about the other nine.)