There's a (non-breaking as far as I know) sequence break you can perform after Venam. I don't know the exact cause but what happened was that after defeating Venam, I bought the Golden Hammer from the AP Store and went to Route 2. I went and triggered the beginning of the Nim event on the route, caught a Crabrawler to aid in my fighting monotype (as Monferno had no chance at 1v3ing Jenkel) but when I went back to fight Jenkel, Karrina was nowhere to be seen, I could enter Jenkel's lab and look at the Pulse Musharna in the machine but Jenkel wasn't around.
I haven't played any further on route 2 so I'll update if there's any future ramifications of this (aside from potentially relationship points).
EDIT: Ok I cannot find Karrina anywhere within Gearen, I don't know if this is normal for v11 or not though.
EDIT 2: Playing with debug I found a fix. The only things I changed were setting the NimTheft variable (036) from 3 to 0 and setting the Quest: Karrina/Dr Jenk (037) variable from 1 to 0