While flying around looking for Better Archeology structures, I came across this in the middle of a lake.
Perhaps adding a water check would resolve this?

BA Version: 1.2.1
MC Version: Fabric 1.21.1 (0.16.10)

This structure uses the Vanilla placement methods, so there must have been a point where a Vanilla structure could also have been placed in that spot.

It appears there was a small island at that location which got covered by the structure. You can see this in the image, as the small river running through it is not part of the structure itself:

At this time, there are no plans to implement a custom spawning method for basic structures.
If more significant issues arise from this behavior, or if there's a known method in Vanilla to include water checks for structure placement, feel free to reopen the issue.