The dog poop seems to be a seperate issue so please use this thread for that: https://answers.ea.com/t5/Bug-Reports/NEEDS-INPUT-CD-Unable-to-use-pet-poop-as-fertilizer/td-p/8539743
As for the other issue, I only see minor differences between the old thread and this one.
It now seems that only the first plant actually gets fertilized while before they all did but with only one fertilizer actually being consumed. To me, the first bug can no longer be in there if we now have this one as they contradict each other. It's like it's evolved.
I will probably need to close the old and leave the new but haven't decided yet.
I have only tested this with normal plants but from what OP describes here and in the original I don't think neither pausing the game nor the quality actually matter for the issue to occur.
@jmeadowbrook I'm unsure I understand your statement about them being wasted. Do you have more than one being consumed but the plant not being fertilized ?
