In my first village, I had all but the Rare yellow pebble.

I got all the collectibles except one beetle with level 3 of exploration. Now I have that and still can't seem to get to the last beetle, and nothing else is happening at all.

I just scroll around while I'm waiting to gain tech points. Which, btw, increase significantly everytime you get a repeat collectable.

In my new village, I have all collectibles except for the rare pink pebble.

Oh, I have to get 2 pebbles, 1 butterfly (the rare pink one) and two beetles

yes, patience...
it took me around 500 hours to finish the collection

*said in a bad impression of William Shatner* One - more - pebble - It's not - showing up. Losing - my mind. Need - that - last - PEBBLE! Where - is it?

im lacking 2 of each collectible rock,beetle,butterflies,and shell

What color is the last rare butterfly??

The answer to that question depends upon knowing which ones you have already found. You can see a picture of the completed collections screen here.