Thank you for the advice.
Of the three currencies, gems can only be acquired by spending money or accruing them slowly by actively playing the game for multiple days.
These particular gems were "free", which means that I got them through spending time instead of money. The overall loss represents about 2 weeks of playing every day. Some were from one-shot rewards, so it is unlikely that I will be able to re-acquire that many in two more weeks of playing.

The problems are:
1. somewhere around 200 missing gems so far, and no recourse to getting any restored. This represents a waste of my time.
2. no logging or message to indicate what the game thinks happened. It could be that it is something that I accidentally clicked on. This "accidental clicking" happens a lot during the lady hunt, for example. (Gosh, it sure would be nice to hide all of those icons.)
3. no acknowledgement of whether this is a known problem or not.

There are several possible ways to resolve this.
1. Tynon could prompt consistently for spending gems. Right now, there are several places where you can accidentally spend gems without a confirmation. Is this what happened? There is no way to know.
2. Tynon could have a log, perhaps in a text file on the computer, of "interesting" things that happen during the game. Spending currency (coin, credit, gem, etc) is interesting. This would be a way for a player to determine what happened during a session. Was it a "player error" or a game glitch?
3. Tynon could take restoring things like gems (even "free gems") more seriously. This implies that Tynon would need to log more things on the server side.
4. To avoid mysteriously losing double-digits of gems, a player can spend gems as fast as they are earned. This implies that items costing more than 10-20 gems are unattainable without spending money.
5. A player can decide that the game is not supported well enough to justify spending multiple hours a day playing.

So, I am left with two choices. Spend gems as fast as I earn them, or stop playing.
The game is enjoyable enough to make this a difficult decision.
Congratulations.