when placing trail runes underwater using commands, it generates air blocks in the water.
how to reproduce :
1. go over a relatively large body of water
2. use the command /place structure minecraft:trail_ruins ~ ~ ~
note :
it does not happen all the time, you have to do it multiple times for it to happen.
Trail ruins are not designed to generate in water; this is not really a bug. The air comes from gravel and sand falling, and processors which "decay" the structure.
The fact generation is weird when it is forcebly spawned in a place it isn't supposed to is not really a bug.