When running with an -nct value greater than 1, the number of times the warning message "HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper, not org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller" appears in the log output can vary from 1 to the value of -nct.
I believe this is because there is no synchronisation on the walkerIdentityCheckWarningLogged variable referenced in: https://github.com/broadgsa/gatk-protected/blob/f185a75e1c49fb4c039511e61254da0509833ee9/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/HaplotypeScore.java#L108-L114