This is typical if you stored items just before a server reset.

Talk to server admin and ask when server gets reset. Reset normally should be done daily to keep server running smooth. Admin can set times and how often, the server I played on did it twice a day.

Basically the game makes a save independent of the server save.
Anything you do between the game save and server reset gets lost.

So if you put items in a chest you lose them.
If you take items out of a chest you duplicate them.
If you harvest a garden they are back.
If you plant a garden they are lost.

So knowing when your online server gets reset and just avoiding playing too close to those times will resolve the issue.
I would typically log out a half hour before reset to avoid issues.