Fallout 4 – Lost voices when talking to follower/characters

The vast majority of companions do not have quests which are required to get a perk. You simply need to max out your reputation.

The exceptions are MacCready, Curie, Cait, and Nick Valentine. You'll need to complete each of their quests to receive their respective perks. While the quests are only offered when you reach maximum affinity, it's possible for affinity to decline between when you are offered the quest, and when you complete it, which means you might not get the perk immediately upon completion of the quest, as both requirements must be fulfilled simultaneously. Simply butter them up a little bit once more to get back to max affinity, and you'll gain the perk.

In my experience if you plant something near the bugged plant, assign a settler to that plant, and let the farming run its course, these issues tend to resolve themselves over time.

I've had invasions occur ON my farm plots, and have watched my missile turrets decimate the farm plots, and then not be able to select the destroyed crops.. Poor farm/defense layout aside, this is the circumstance in which I came back later and notice that the plants were eventually revived.

In short, I wouldn't worry so much about micro-managing the efficiency of every single plant. If food and water is sufficient for stability or growth, that's good enough for me!