What we're dealing with is the sort of inability to really understand the most basic processes that causes Elly to eventually translate what normal people would understand as meaning "You stupidly destroyed what you were working on because you have no idea what you're doing" into "You were right all along." This, I should think, is why she never understood that her old boss was trying to tell her that she couldn't afford to pay her and it's a lot of the reason why she's such a dubious mother and pet owner. To put it as simply as possible, Elly has never quite understood what the people around her are doing and why they do it.
This sort of inability to really understand what's going on is, as I've said, akin to her and John's inability to make a connection between their baffling refusal to share their interests with their children and the fact that the kids don't share their interests. It's like how Curtis's dad can't understand why his son thinks work is the worst thing ever merely because he spends his free time wailing about how hard his life is and how the working man is the victim of all victims surpassing all others. In both cases, idiot parents are angry at children for stupid reasons because they don't understand that they're being stupid.