As mentioned by PNibbles
and confirmed by izret102
, an update "now displays missed scarabs on the map. They appear as light blue circles with a vertical line down the center."
Scarabs are found in some of the pinball sections and initially their wings are closed. As you complete the requirements for their section of the pinball area (lighting up nodes) they will start to open their wings. This can sometimes take anywhere from 2-5 cycles. When the scarab is completely opened, fruit will burst out and the scarab will completely disappear if you go far enough away and come back.
While not a solution, I'd recommend that you be aware of this (secret) achievement and work on completing all the scarabs as you work your way through the game. Of course, this doesn't help if you don't know that you need them.
As far as I know, there are no in-game map items that will display scarabs on the overworld map like there are for chests and wickerlings, but IGN has a map that is useful for mopping up. http://www.ign.com/wikis/yokus-island-express/Scarab_Locatio...