It's not an issue with FWE because I have the same issue and I don't have FWE installed at the present time. I have MMM, which I assume you do too? Or is respawing built into FWE... Not sure if MMM is the root cause or just creates an opportunity for an exe bug to present itself.
Found and fixed the problem. It should be considered an MMM fix.
MQ01CitySuperMutant needs to have the "Use AI Data" flag turned on so that it uses the AI Data data from the template it's using.
The second mutant that is there (MQ01CityMutantSpineBreaker02) uses MQ01CitySuperMutant as it's template and had the "Use AI Data" flag turned on, so it is ok. It gets it's AI Data from there. But because MQ01CitySuperMutant wasn't getting/using the proper AI Data it messed up that second mutant.
All the other super mutants in that area MQ01SchoolSuperMutant01 to MQ01SchoolSuperMutant07 all have the "Use AI Data" flag turned on and are fine. The remaining 3 MQ01 mutants in that area seem to be one time only appearance mutants and are fine as well.