Is my contractor doing a botched up job installing the soffit
Vinyl expands and contracts as temperatures change. As long as the vinyl can move as required, staples could work, although not my choice, roofing nails driven by hand is my preferred method of fastening. If one leg of the staple is in the slotted hole and the other beyond the edge, and it is not tight to the plywood so there is a little room for movement, the staples will work. If the leg of the staple is IN the vinyl, it is locked in place, and will not move as needed. The very short pieces that are nailed in that way can be the exception, since they are so short, movement will be negligible. Also for what it is worth, one staple can be driven to lock an end or middle in place, as long as the rest of the staples allow the vinyl to move elsewhere.

Just as a mention, why is the installer putting up vented soffit when the backer is solid. The perforations will be of no use. Typically the soffit goes directly to the framing if the soffit needs to be vented....