This is very easy to reproduce. Place two combinators, one vertical and another horizontal. Copy settings from one to the other and the orientation changes.
Would not be that bad if I could rotate it back but since rotate only changes input/output side...
Thanks for the report, This will be fixed in 2.5.3 It is related to copy assembler pipe direction. I have changed it to only rotate if there are fluidboxes AND it is a square collision box.
