This gets spammed in my log file so I assume the issue lays somewhere in here, I do not know a lot about the log file but I have a basic understanding of programming.
It basically always happens for me, in VAB/SPH and in flight, no matter what vessel I test it on. No other mods installed, only MechJeb.

[LOG 04:12:07.176] [MechJeb2] Exception in MechJebModuleStageStats.StartSimulation(): System.TypeLoadException: Could not load type 'ModifierStagingSituation' from assembly 'Assembly-CSharp, Version=0.0.0.0, Culture=neutral, PublicKeyToken=null'. at MuMech.FuelNode.Init (.Part part, Boolean dVLinearThrust) [0x00000] in <filename unknown>:0 at MuMech.FuelNode.Borrow (.Part part, Boolean dVLinearThrust) [0x00000] in <filename unknown>:0 at MuMech.FuelFlowSimulation.Init (System.Collections.Generic.List 1 parts, Boolean dVLinearThrust) [0x00000] in <filename unknown>:0 at MuMech.MechJebModuleStageStats.StartSimulation () [0x00000] in <filename unknown>:0 at MuMech.FuelNode.Init (.Part part, Boolean dVLinearThrust) [0x00000] in <filename unknown>:0 at MuMech.FuelNode.Borrow (.Part part, Boolean dVLinearThrust) [0x00000] in <filename unknown>:0 at MuMech.FuelFlowSimulation.Init (System.Collections.Generic.List 1 parts, Boolean dVLinearThrust) [0x00000] in <filename unknown>:0 at MuMech.MechJebModuleStageStats.StartSimulation () [0x00000] in <filename unknown>:0

Issue fixed after updating KSP from version 1.1.0 to 1.1.2.
If this is an issue for 1.1.0 please do not advertise mod as compatible with 1.1.0 on Curse.

That error could only appends if you played with the pre release instead of the 1.1 final release.

Don't complain about compatibility if you don't use the proper version.