I don't think it's fair to simply assume all is right and well at ND, but it's also not fair to look at everything as if everything is part of some nefarious plotline.
Are there issues at ND? Frankly, we don't know, but we can infer that there were some issues at the highest level of management with Amy Hennig, which means that the influences of that problem, will rationally extend to ND employees who's probably close to Amy, or have suffered some setbacks because of said situation. (team Uncharted)
But the last 2 departures, Wells and Knowland, were departures that would be kind of a left-field to associate with the so-called trouble at ND. Heck, they've only joined for a short few years, and were not in the same team anyway as they've been solely working on TLoU.
For what it's worth, I don't see any indication that other leads from the Uncharted team like Josh Scherr, Kurt Merganau, Jeremy Yates or Taylor Kurosaki leaving. Those departures would be also extremely huge, as 3 of said UC4 leads are also ND veterans who's been there for more than 10 years.