Raphael spends much of the film in a suit of armor, terrorizing the criminals of the neighborhood and seems to enjoy the fear that comes with it, with Leonardo disliking the Nightwatcher due to his methods. Given their most famous enemy, Shredder, tends to pride himself on being feared, Leonardo might feel the Nightwatcher is similar to their arch-enemy, who Raphael is unintentionally emulating.
For double brilliance, this works as a Mythology Gag, since Raphael did assume Shredder's identity in the comics.
Perhaps even Splinter realize this, hence why he solemnly tells Leo, who goes out to find Raph, that he "know[s] what [he has] to do".
Since the film is supposedly in the same continuity as the previous live-action movies, April changing occupations makes sense when you take into factors in the first two movies. She was frustrated with her boss Charles Pennington telling her to stop hassling Chief Sterns for his inaction, then she suddenly gets fired and presumably remains unaware why (Charles was blackmailed by Sterns to get April to back off and he'll erase Danny's criminal records), only that "there are circumstances". In the second movie, her other manager care more about ratings and try to get her to do a story on swimsuits, when she wishes to continue investing T.G.R.I. to help the Turtles. So the obstruction of news-reporting caused her to quit in disgust, and chose a career in archeology (which may have been her father's job in this continuity since he owned antique store before it was set on fire).