Motion 3.0.2. I edited text. Then I moved three objects further down the timeline. Whoops, made a mistake. Undo. The text gets unedited, but the three objects are still further down the timeline. Wha? Further undos just undo other timeline edits to the objects, but relative to their new not-undone changed positions.
That probably sounds pretty confusing, but put simply: anyone else having random undo issues, seeming to be out of order?
Try trashing the motion preference file. Also it might not be a bad idea to set the auto save to about every 5min that way if it still does not let you properly undo you can always revert to a auto save.
There are no "technical solutions" to your "artistic problems".
Don't let technology get in the way of your creativity!