Running two instances of any of the VIs related to Estimation VI palette will cause the instances to conflate signals.
Running two instances of any of the VIs related to Estimation VI palette in Control & Simulation->Simulation will cause the instances to conflate signals. This is because the VIs are set to Shared Clone Reentrant Execution.
Manually set the necessary VIs in \LabVIEW 20xx\vi.lib\Simulation\Estimation\Implementation to Preallocated Clone Reentrant Execution.
LV Control Design and Simulation: 2017
LabVIEW 2020 Control Design and Simulation Module
May 20, 2018