More details would be needed to troubleshoot the issue. like logs from both the client and the server. Going to move this thread over to the support section. Check the pinned topic on how to report an issue for instructions on providing logs via Pastebin.
Originally posted by Arctic Ice Fox: Me and my friend had the same "bug" its the whole weight system. Crop plots are bad at supporting weight (dont know the numbers off the top of my head) and sometimes when the game reloads a chunk something goes weird and they fall in. We found that by putting wood/concrete/cobble plates below the crop plots it fixed the problem entirely.
Wait, so what did you have before that fix? A ceiling composed solely of farm plot blocks?