Mr. Monk Is Underwater - S7-E5
Character mistake: Commander Whitaker asks what Monk and Natalie are doing on his "ship." No submarine commander would ever refer to his vessel that way. He would refer to it as his "boat."
Mr. Monk and the Genius - S7-E2
Character mistake: At the beginning when Monk is writing Natalie's check, we see a shot of it, but the I in "nine" isn't dotted. As meticulous as he is, Monk would never leave an I undotted (we've even seen him dot someone else's i) especially since it would bother him.
Answer: Stottlemeyer was already upset after the phone call. He was trying to get "Kevin" (who would have to be a judge, but no further character information is given) to issue a restraining order with no evidence of needing one, except that Adrian Monk said she needs one. Kevin said he would need to "sleep on it." So it's clear they've been trying to provide protection and unable to get the results they need, which seems to be based on no one trusting Monk the way Stottlemeyer does. He's just angry that they failed to protect Linda despite all their work. Although it does feel like a scene was cut, or altered, from the show that shows the futile attempts to protect Linda which built up to his outrage.
Bishop73