Please provide a repeatable process to reproduce this bug. Thanks.

ok well
it went like this
sounds really dumb but just keep saving until it happens

yeah sorry but its still happening
well to put it in a better way:

step 1 have a build on for a long time, maybe 30 minutes.
step 2 save repeatedly over and over again.
step 3 look around for suddenly misaligned parts. (this glitch may happen sooner than you think)

sorry but its a really annoying glitch, otherwise your software is fine.