Issues like this can happen after you had generated the LOD and especially through CK, CK tends to damage the wordlspace, so you need to back up yor esp > generate LOD > overwrite your esp with the back up.
Damaged esp / worldspace after generating LOD can't be undone, neither with Tes5Edit, you need to start over.
If you haven't generated LOD, then re-adjust the 'Water's Height' of that cell and do not use a 'save file' that has seen the mod or cell, use 'COC' or 'COW' from the "Main Menu" to test / check the cell's building progression without loading a save.
Other than that i can't think of a reason right now what could be the reason for that.
Edited by maxarturo, 09 June 2021 - 08:40 PM.