Umps are normally way off base but I honestly don't see much wrong here. I'd need to get clarification on what Francona was arguing but HBP is a reviewable play. If he still has his challenge then challenge, if he doesn't then the umps aren't allowed to use a crew review until the 8th. They got together and discussed it and felt it wasn't a HBP which appears to be the correct call. If that was indeed the discussion the umpire gave him a lot of rope on a pretty black and white decision. Either sit down and we can continue the game or you're I'll make you sit down somewhere else.
As for the 2nd one I don't believe I've ever seen a pitcher get a handful of warmup pitches after a 5 minute delay because of a ruling/arguing. I'm not sure if the umpires have the discretion to allow it. Looks like Tepera got some there at the end so I guess so unless he went rogue after the ump was distracted tossing his manager. Tossing Nevin was a bit much in that spot and a lot likely could have been done to calm the situation down rather than escalate but he was likely still hot after whatever the hell Francona decided to get upset about for no reason.