Is anything else going missing at all? (Likely candidates would be heads, skins, stuff in the stash…)
There are a couple of ways to accidentally use lots of moonstones. One would be accidentally selecting Luneshine grind at the grinder - the higher the level of items being ground, the more moonstones that get consumed when you do that. The other is the grey Dahl large chests that look identical to the large red ones - they cost moonstone to open (like the Tiny Tina Dice Chests in BL2)
It it’s only the moonstones missing (and you’re not seeing other stuff gone of having your progress reset) then my guess would be you’ve tripped up on the latter stuff. If you are missing more than just moonstones, it sounds like your save files are either getting corrupted or over-written.