the only place he could

It's a Jedi ship. It's got a workbench with the materials and tools to build a lightsaber. Is it really that far fetched that she might store a kyber crystal in there somewhere as well?

Or that she has a spare lying around in case she lost one of hers so she can build a new one?

She even has huyang on board. Maybe they flew out and got some at one point. Maybe it's a crystal from a lightsaber she collected from a Jedi that died.

Maybe it's from her original lightsaber.

Plenty of plausible reasons why she could own another crystal.