That Bug is happening to me too (KSP 1.2.2). I've read in the changelog that this bug should be gone with the new version of TweakScale for KSP 1.3, but i want to stick a little bit with my modded KSP 1.2.2 Version.
It happens when you shrink a Part and the MFT-Module is in that part present. If you shrink too much, the mass becomes negative and this breaks Physics.
My Workaround: Don't shrink that much, so that the mass of this part becomes negative; check your MJ / KER for these changes in mass. I know this is suboptimal (and a little bit of a cheat, but i'm playing with RSS ...) but its ok for me till i update to 1.3 and this will begone hopefully. PS: see also http://forum.kerbalspaceprogram.com/index.php?/topic/99956-wip-tweakscale-development-thread/&page=18#comment-2997401