I planted marigolds and they've been doing good, but today I noticed as I was watering my flowers they were gone. And I have about 3 med sized holes near the flower bed. And then I came up to the flowers and the place where the marigolds were there were holes under neath..so I'm confused what would take just those flowers?

Is there anything left, like a stump? Look under some nearby plants and see if the remains of the marigolds are there. I once had voles take a whole bed of marigolds and they dragged them to the cover of nearby plants where they could feed on them in safety.