Yes you can say it's "another misunderstanding plot," in the same way that "there is no new thing under the sun."
Misunderstanding is not just a manga trope, it can occur between any two people in real life; there are a lot of problems caused by humans not able to share mind over wifi. What's important is they come in a lot of variations.
IMO misunderstanding is only a bad trope when it should be resolved by simply having them sit down and explain. We all hate it when it won't even take 15 seconds to clarify, but instead the pair avoided each other till the end of the time. (Even worse if it's out of character to do so.)
This chapter is nothing like that. Touko reached out, they walked in the wood a bit and respectively realized there's nothing to say. They are struggling to find a positive reason themselves:
Touko is moving on and no longer relies on Yuu as the life-saving raft; having never experienced love, Yuu is self-doubting -- if my feeling is not love, is it better to let go of Touko so she can move on?
It's not like they have anything to contribute to the situation.
They wouldn't try to come back together because it may actually be better to be separate.
Dammit, at this point it's more natural for them just to gradually let go, and I'm willing to swallow one or two forced plots for them to get back together.
A stereotypical "misunderstanding plot" (at least the ones I hate) is not this kind of magic.
In the end, persuasion cannot change hate into love. If you already dislike this trope, keep doing that -- it's good to have preferences.
But I hope to clear up some confusion for people who think "what the heck why are they behaving like this." I found these to be pretty well based.