Autofocus is complex....there are multiple modes, multiple ways to control the camera; for example, at times back button focus is enabled, and a person can have an "AF problem" when they expect that the shutter release button should control the focus. Or the focus is set to AF-A, which is a horrible,horrible, incredibly stupid thing Nikon created. I dunno...I own a D610...I am not fond of the camera's AF setup or system. it's not what I am used to. I don't like the 39 AF points, I prefer the higher-end 51-point systems; the 39-point system was, I think borrowed from APS-C models, and is not appropriately spaced for a larger frame area.
As a good example of the complexity of AF systems, AC12's post right above this one details "some" of the complexities and foibles that can enter into AF problems. Since the lens has been repaired twice, there's the possibility that the issues lie with either the camera or the shooter, or a little of both.
Another aspect is the use of ONE, single AF point...many people advocate that. I do not. But also, there's two very-basics ways to use Nikon AF, and multiple variations. But, as to the two basic ways: one is to allow the camera to select the AF point/target, the other is for the shooter to initially select the desired target, using the 4-way thumb controller on the back of the camera. The user selects the target, for each series of shots, then the camera can track the subject anywhere across the frame. The issue is that 1) users often do not select the target 2) the focusing is poor.
Because modern d-slrs are so complex, I suggest doing a two-button reset of the D610, and starting from scratch. My gut feeling as a 17-year Nikon d-slr user is that your wife's camera and custom functions and settings are messed up, and secondly: I have a strong suspicion that she's got the camera setup that allows AF-A, which screws up more shots than it has ever saved. Search YouTube for the video that tells you how to get-rid of AF-A on the D610.
I would strongly recommend that she buy Thom Hogan's Complete Guide to the Nikon D610; the AF system is complicated enough that it requires a plain English user manual to navigate.
A link that might be of some help:
What is the difference between AF-A, AF-S, AF-C and MF focus modes on Nikon camera's. When should you use AF-A, AF-S, AF-C, MF. - SLR Photography Guide
Here's where I suspect the problem lies: "
The default camera setting is AF-A. As mentioned earlier, this mode guesses if the subject you are photographing is stationary or moving, and accordingly sets the focus to either AF-C or AF-S. Photographers don’t always trust the camera to pick the correct setting, preferring to make the choice themselves."