In some cases, it’s not actually a bug. In some cases, it’s because the game has not saved.
Use /save-all before you restart(or do any changes to) the server.
This saves anything you’ve done with plugins, player data (their location, inventory, health etc) and world data.
If you have auto save enabled (/save-on) It autosaves every 6000 ticks. (300 seconds / 5 minutes).
Kits however, is a issue I’ve encountered too. Mostly with Deathmatch kits. They tend to reset all the time the server turns off -_-