Ah, another victim of the mythical dead spots. Sorry for the incredibly long post, I wanted to make sure it was clear. Still not sure it is, though.
The problem is that before growing, a bush will check its surroundings. There are two main rules, and I think the second one is your problem here. When growing, it will check for this:
The connecting plants limit.
To prevent people from boxing in houses with trees and bushes, no more than twelve plants can be in a single line. This, of course, includes diagonals. Try counting all of the trees and bushes that it will be connected to (Including those diagonal of other plants).
The plants per acre limit.
There is a limit to the amount of trees and bushes that you can have in a given space. When a new tree or bush is grown, it will check all around it, looking for other trees and bushes. For trees, this is rumoured to be a 7x7, like this:
□□□□□□□
□□□□□□□
□□□□□□□
□□□■□□□
□□□□□□□
□□□□□□□
□□□□□□□
For bushes, however, it could very well be a big plus sign, more like so. I'm not sure yet, I want to test this at some point.
xx□xx
xx□xx
□□■□□
xx□xx
xx□xx
(x = not checked)
When too many trees or bushes are detected in these areas, it will shrivel up and die a lonely death.
So how do you prevent this?
The only real way around this is to work slowly, from top to bottom, only planting one plant per day. Usually, this will work, as long as you are not trying to have more than twelve plants connected.
Example!
You have a perfect pear farm. Yay, pears. Nine trees, like this:
■□■□■
□□□□□
■□■□■
□□□□□
■□■□■
The middle one dies, so you want to replant it. no big deal, right? You've replanted a tree on the side before, and that worked, so it should grow. Except it doesn't.
Pick a tree, any tree - except the middle one. Look all around it, in a 7x7 square like I showed you. Imagine that, beyond the farm, all squares are empty, and at most, you will find five trees.
But replanting the middle one does not work. It will check, see eight neighbours, tries to imagine having to greet them all in the morning and dies of its social anxiety.
So how did it grow in the first place? Well, the answer is simple. When it was planted, not all of the neighbours had moved in yet. Most likely because the farm was put there from top to bottom row by row, and the first time it grew, it only had five neighbours. Which was fine. But now, it's not.
Advice:
You need to redo a lot of those, work slowly, from top to bottom. It sucks, I know. :c