I don't know if this is a bug or vanilla behaviour of TFTD.
When you have a unit standing outside next to a ship, then selecting a view level which makes the roof appear will block the animation of bubbles if they normally would animate on top of the roof graphic. You would obviously want to block the appearance of bubbles for units inside the ship when the roof is showing, but presumably not block the bubbles for units standing outside the ship. I've only tested this with 1-level ships (e.g., Triton or small Alien craft).
Occurs in the latest gitbuild 2015_08_24_0859. Anyone know if this something in Vanilla TFTD or is it specific to OpenTFTD?
Cheers,
igtc