Bricks or blocks mortared in to fill the holes.

Hydraulic cement expands a bit as it cures, it's a good choice for "filling things in".

If the volume is excessive you can use a few small bricks or something similar to bulk up the interior volume of the cavity, then fill the remainder with the hydraulic cement.

Mongo

You can form one side by cutting plywood larger and tapcon screwing into the existing. You shouldn't have to form the opposite side if you run your mix "dry" or sticky, not too much water. You might want to throw a little mesh wire in there around the half way point when filling. Then put a waterproofing sealer/coating in and around the area of the flower bed, something such as drylok or thompsons.

Be very careful if these are vents to a crawlspace, which is what is sounds like. You don't wan't to create moisture problems for yourself. You are also potentially creating issues with a soil buildup around your foundation. Done incorrectly, it is a direct invitation to termite infestation as well as a direct route for more moisture into your crawlspace/basement.