The whole thing with Mio isn't even forced, it was pretty obvious that Yuuji's secret interactions with Mikako would eventually pop up, and considering the considerable amount of trauma Mikako caused, it was never going to be a pretty interaction.
Mio ran away because she thought Yuuji was becoming friendly with the ex-friend that ruined her trust in people through the bullying she induced Mio to, Yuuji and family went out to search for Mio and Yuuji's sister helped to clear up the misunderstanding and push Mio to do something she was afraid to do alone... And their friends bonded over fixing a mistake made while working in the office (it was a weird jump cut that felt out of place, though it might have been meant to establish that often the things we think are world ending issues have simple solutions and aren't that big of a deal, much like how Mio was overthinking the issue with the voicemail Yuuji received.)
Idk, it seems pretty obvious with the inner monologue about how she was just starting to trust people again when this all happened. It makes sense that Mio would be freaked out because her friend betrayed her, bullied her and destroyed her most treasured possession, it's pretty hard to trust others when you get so severely betrayed by someone close to you (it's implied that Mikako used to pretty much be her only friend during that flashback,) thus the trauma made her afraid that Yuuji was going to repeat the past and betray her too. There are a lot of confusing things about this series, I'm kind of surprised this is being considered one of them since it's pretty straightforward unless you forgot who Mikako was.
It's not the first time she's freaked out when she thought Yuuji made a friend, is the thing. It's hard to follow because her trauma is irrational, and only ever gets brought up after Yuuji gets a phone call from someone. Then it's explored in vague snippets, then resolved with some unrelated gesture. I spent ages agonizing over what she's said, and I really didn't understand the issue. She never said, or even implied, that it was that he was talking to her bully, or that he'd repeat the issue. The closest we have to an explanation is that he told a single lie to, as she already knows, avoid opening up old wounds.
I had different things to say to each person as I went through the comments, nothing wrong with multiple comments to different people. Also, idk, I'd still say that this incident is pretty straightforward if you have a basic understanding of how trauma works, but this series has had a lot of other parts that were rather confusing, so I don't fault you for getting lost along the way, I just wanted to surmise the issues at hand since it seemed like a lot of people were missing something that seemed pretty straightforward to me, though I admit I probably have a lot more knowledge and experience with how different people react to trauma and such than most (I have ptsd from a car accident I was apart of and I know other people with ptsd and other forms of anxiety from various other kinds of incidents, some similarly involving incidents with toxic people)
