When you use content which costs Crystals, Free Crystals are spent first. If you don't have enough Free Crystals, Paid Crystals will be spent.
Please check whether you might have used content that requires Crystals, such as gacha, restoring Bonus Energy, or the Virtual Shop, without having enough Free Crystals to pay any necessary cost.
The number of Crystals shown in the upper right corner of the Gacha screen indicates the total number of Paid and Free Crystals.
When Paid Crystals are spent, the total number of Paid and Free Crystals, which is displayed underneath the number of "Paid" Crystals, is also reduced by the same amount.
Specifics regarding Paid/Free Crystals can be found from Menu > Purchase Info
If the above does not solve the problem, please contact us from Menu > Support.