Negative Skill Points

For some reason my players are experiencing negative skill points. Is there something in the config? I only numbers I changed is the amount it takes to get to tier 2 & 3 skills. I will upload the config as well. 

SkillTree.json

I cannot think of a single reason that a player would get negative xp, outside of losing xp on death and going into xp debt, but that looks a lot different.

I wouldn't even know where to begin to check where the issue lies; need more information about how this has occurred.

Player incident: 

"I was mining for ores in the desert, had to log off so I hid in a ditch and disconnected. Came back and I was dead and it was negative -1000 and kept decreasing up to -12000."

"i was crafting when i lost points still losing points for crafting."

Crafting is the most common that I hear about losing xp.

Changed Status from Pending to Closed