When going from Cerulean to Vermilion, i always have to go back after like 2 battles... First, there's the Butterfree guy, that thing is sometimes pretty evil. Then, there's the 3 Pidgeys Lass, if i'm underleveled, she can annoy the hell out of me with Sand-Attack. And then, there's the Raticate dude, not as hard as the Raticate rocket in Mount Moon, but as a <20 Raticate it's still ridiculously overpowered.
Rock Tunnel isn't that bad, the last trainers in Rock Tunnel are rather weak ones, the ones after Rock Tunnel can be easily avoided.
But i hate the routes near Snowpoint, i mean, if you're battling a trainer with 4 Snovers that all use Ice Shard while it hails, and only have one Pokemon, it's hell. Seriously.
Can't think of anything similar now, but i'm pretty sure there are a lot of similar places i just forgot now.