If Your Numbers Don't Match:

If you caught more than 46, the extra ones are probably the ones you failed to catch on previous days, if you caught less than 46, you probably missed some, sometimes they don't spawn right away, you have to TP again for the bugged spot to trigger.

Some of the spawn spots are one-time, which makes you go beyond 46 geniemons. But the number should fall back to 46 after you deduct the one-time spawns.

For Exploration:

As of 1.0, geniemon and all other events in Exploration might be bugged.

Commission Spawns:

After the event triggers 15 times, you might experience increased difficulty for them to spawn. You can do a few more runs to check, if nothing spawns over multiple runs, Lulu Theft treasure event and/or Expedition event in openworld might got counted towards your weekly cap. It is recommended to do Extermination (Weapon Book EXP) since it doesn’t have Lulu Theft event. As for Expedition event, there’s nothing you can do.

*Edit: Fixed missing spots in Purgatario Island, added description above into the image.