I have a garden of pumpkins and melons. Recently, I noticed less and less bees and beetles pollinating the flowers. It dug under my electric fence and has been eating baby melon, baby pumpkins, and flowers. It kills all the bugs that pollinate my flowers and I now have almost no pumpkins and melons. It digs under my plants, and leaves black dots everywhere. I have no clue what creature does this. I live in MO, or Mmissouri. It cones at night and am at a loss on what to do. I block all it's holes and barricade the entrance.

Some pics would be helpful, why do you think it kills the pollinators?

You need a critter cam. I got one a few years ago because I couldn't figure out what was chewing on my drip lines (squirrels and coyotes). I was astounded by the number of critters walking through my yard at night.

Groundhogs dig and they eat pumpkins and pumpkin plants.
The dots, I suspect a different problem. And probably neither directly affects bees.
Can you post pictures of black dots or damage?

I place a havahart trap next to the fence facing the entrance where varmints are burrowing under.
I don't even have to bait.
The unwanted animal comes for it's evening raid and gets stopped.
When I trap a problem animal that nobody wants released at their house, I shoot and bury... Some things are illegal to trap and dump...

When I trap a pet, I open the cage and set it free unharmed.
It's important to check traps very early... by flashlight... Armadillo will tear the trap apart if left too long.

Pictures of the damage would help us figure out what is going on.

As suggested above, a trail cam would help you figure out what is going on (its also amazing to see what is happening at night). Alternatively check for footprints, you might be able to identify the culprit that way. You might want to rake and water the area to make the footprints more obvious.

Regarding the pollinators; this is the time of the year when their numbers naturally start to decrease. With fewer sources of food due to the cooling weather the number of active bees and other bugs decreases. I don't think the reduced number of bees is related to whatever is eating your squash.